L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)
head(L1000_signature_data)
        AARS ABCB6 ABCC5 ABCF1 ABCF3 ABHD4 ABHD6 ABL1 ACAA1 ACAT2 ACBD3 ACD ACLY ACOT9 ADAM10 ADAT1 ADCK3 ADH5 ADI1 ADO ADRB2 AGL AKAP8 AKAP8L AKR7A2
10-DEBC    0     0     0     0     0     0     0    0     0     3     0   0    0     0      0     0     0    0    0   0     0   0    -3      0      0
        AKT1 ALAS1 ALDH7A1 ALDOA ALDOC AMDHD2 ANKRD10 ANO10 ANXA7 APBB2 APOE APP APPBP2 ARFIP2 ARHGAP1 ARHGEF12 ARHGEF2 ARID4B ARID5B ARL4C ARNT2
10-DEBC   -3     3       0     0     0      0       0     0     0     0    0   0      0      0       0        0       0      0      3     3     0
        ARPP19 ASAH1 ASCC3 ATF1 ATF5 ATF6 ATG3 ATMIN ATP11B ATP1B1 ATP2C1 ATP5S ATP6V0B ATP6V1D AURKA AURKB AXIN1 BACE2 BAD BAG3 BAMBI BAX BCL2 BCL7B
10-DEBC      0     0     0    0    0    0    0     0      0      0     -3     0       0       0     0     0     0     0   0    0     0   0   -3     0
        BDH1 BECN1 BHLHE40 BID BIRC2 BIRC5 BLCAP BLMH BLVRA BMP4 BNIP3 BNIP3L BPHL BRCA1 BTK BUB1B BZW2 C2CD2 C2CD2L C5 CAB39 CALM3 CALU CAMSAP2
10-DEBC    0     0       0   0     0     0     0    0     0    0     0      0    0     0   0     0    0     0      0  0     0     0    0       0
        CANT1 CAPN1 CASC3 CASK CASP10 CASP2 CASP3 CASP7 CAST CAT CBLB CBR1 CBR3 CCDC85B CCDC86 CCDC92 CCL2 CCNA1 CCNA2 CCNB1 CCNB2 CCND1 CCND3 CCNE2
10-DEBC     0     0    -3   -3      0     0     0     0    0   0    0    0    0       0     -5      0    0     0     0     0     0     0     0     0
        CCNF CCNH CCP110 CD320 CD40 CD44 CD58 CDC20 CDC25A CDC25B CDC42 CDC45 CDCA4 CDH3 CDK1 CDK19 CDK2 CDK4 CDK5R1 CDK6 CDK7 CDKN1A CDKN1B CDKN2A
10-DEBC    0    0      0     0    0    0    0     0      0      0     0     0     0    0    3     0    4    0      0    0    0      0      0      0
        CEBPA CEBPD CEBPZ CENPE CEP57 CERK CETN3 CFLAR CGRRF1 CHAC1 CHEK1 CHEK2 CHERP CHIC2 CHMP4A CHMP6 CHN1 CIAPIN1 CIRBP CISD1 CLIC4 CLPX CLSTN1
10-DEBC     0     0     0     0     0    0     0     0      0     0     0     0    -4     0      0     0    0       0     0     0     0    0      0
        CLTB CLTC CNDP2 CNOT4 CNPY3 COASY COG2 COG4 COG7 COL1A1 COL4A1 COPB2 COPS7A CORO1A CPNE3 CPSF4 CREB1 CREG1 CRELD2 CRK CRKL CRTAP CRYZ CSK
10-DEBC    0    0     0     0     0     0    0    0    0      0      0     0      0      0     0     0     0     0      3   0    0     0    0   0
        CSNK1A1 CSNK1E CSNK2A2 CSRP1 CTNNAL1 CTNND1 CTSD CTTN CXCL2 CXCR4 CYB561 CYCS CYTH1 DAG1 DAXX DCK DCTD DCUN1D4 DDB2 DDIT4 DDR1 DDX10 DDX42
10-DEBC       0      0       0     0       0      0    0    0     0     0      0    4     0    0    0   0    0       0    0     0    0     0     0
        DECR1 DENND2D DERA DFFA DFFB DHDDS DHRS7 DHX29 DLD DMTF1 DNAJA3 DNAJB1 DNAJB2 DNAJB6 DNAJC15 DNM1 DNM1L DNMT1 DNMT3A DNTTIP2 DPH2 DRAP1 DSG2
10-DEBC     0       0    0    0    0     0     0    -4   0     0      0      0      0      0       3   -3     0     0      0       0    0    -3    0
        DUSP11 DUSP14 DUSP22 DUSP3 DUSP4 DUSP6 DYNLT3 DYRK3 E2F2 EAPP EBNA1BP2 EBP ECD ECH1 EDEM1 EDN1 EED EGF EGFR EGR1 EIF4EBP1 EIF4G1 EIF5 ELAC2
10-DEBC      3      0      0     0     0     0      0     0    0    0        0   0  -3    0     0    0   0   0    0    0        0      0    0    -3
        ELAVL1 ELOVL6 EML3 ENOPH1 ENOSF1 EPB41L2 EPHA3 EPHB2 EPN2 EPRS ERBB2 ERBB3 ETFB ETS1 ETV1 EVL EXOSC4 EXT1 EZH2 FAH FAIM FAM20B FAM57A FAM63A
10-DEBC      0      0   -3      0      0      -3     0     0    0    0     0     0    0    0    0   0      0    0   -3   0    3      0      0      0
        FAM69A FAS FASTKD5 FAT1 FBXL12 FBXO11 FBXO21 FBXO7 FCHO1 FDFT1 FEZ2 FGFR2 FGFR4 FHL2 FIS1 FKBP14 FKBP4 FOS FOSL1 FOXJ3 FOXO3 FOXO4 FPGS FRS2
10-DEBC      0   0       0    0      0      0      0     0     0     0    0     0     0    0    0      0     0   0     0    -3     0     0    0    0
        FSD1 FUT1 FYN FZD1 FZD7 G3BP1 GAA GABPB1 GADD45A GADD45B GALE GAPDH GATA2 GATA3 GDPD5 GFOD1 GFPT1 GHR GLI2 GLOD4 GLRX GMNN GNA11 GNA15 GNAI1
10-DEBC    0    0   0    0    0     0   0      0       0       0    0     0     0     0     0     0    -4   0    0     0    0    0     0     0     0
        GNAI2 GNAS GNB5 GNPDA1 GOLT1B GPATCH8 GPC1 GRB10 GRB7 GRN GRWD1 GSTM2 GSTZ1 GTF2A2 GTF2E2 GTPBP8 H2AFV HADH HAT1 HDAC2 HDAC6 HDGFRP3 HEATR1
10-DEBC     0   -3    0      0      0       0    0     0    0   0     0     0     0      0      0      0     0    0    0     0     0       0      0
        HEBP1 HERC6 HERPUD1 HES1 HIF1A HIST1H2BK HIST2H2BE HK1 HMG20B HMGA2 HMGCR HMGCS1 HMOX1 HN1L HOMER2 HOOK2 HOXA10 HOXA5 HPRT1 HS2ST1 HSD17B10
10-DEBC     0     0       0    0     0         0         0   0     -3     0     0      0     0    0      0     0      0     0     0      3        0
        HSD17B11 HSPA1A HSPA4 HSPA8 HSPB1 HSPD1 HTATSF1 HTRA1 HYOU1 IARS2 ICAM1 ICAM3 ICMT ID2 IDE IER3 IFNAR1 IFRD2 IGF1R IGF2BP2 IGF2R IGFBP3
10-DEBC        0      0     0     0     0     0       0     0     0     0     0     4    0   0   0    0      0     0     0       0     0      0
        IGHMBP2 IKBKAP IKBKB IKBKE IKZF1 IL13RA1 IL1B IL4R ILK INPP1 INPP4B INSIG1 INTS3 IPO13 IQGAP1 ISOC1 ITFG1 ITGAE ITGB1BP1 ITGB5 JMJD6 JUN
10-DEBC       0      0     0     0     0       0    0    0   0     0      0      0     0     0      0     0     0     0        0     0     0   0
        KAT6A KAT6B KCNK1 KCTD5 KDELR2 KDM3A KDM5A KDM5B KEAP1 KIAA0100 KIAA0196 KIAA0355 KIAA0753 KIAA0907 KIAA1033 KIF14 KIF20A KIF2C KIF5C KIT
10-DEBC     0     0     0     0      0     0     0     0     0        0        0        0        0       -4        0     0     -3     0     0   3
        KLHDC2 KLHL21 KLHL9 KTN1 LAGE3 LAMA3 LAP3 LBR LGALS8 LGMN LIG1 LIPA LOXL1 LPAR2 LPGAT1 LRP10 LRPAP1 LRRC16A LRRC41 LSM5 LSM6 LSR LYN LYPLA1
10-DEBC      0      0     0    0     0     0    0   0      0    0    0    0     0     0      0    -3      0       0      0    0    3   0   0      3
        LYRM1 MACF1 MALT1 MAMLD1 MAN2B1 MAP2K5 MAP3K4 MAP4K4 MAP7 MAPK13 MAPK1IP1L MAPK9 MAPKAPK2 MAPKAPK3 MAPKAPK5 MAST2 MAT2A MBNL1 MBNL2 MBOAT7
10-DEBC     0     0     0      0      0      0     -4      0    0      0         0     0        0        0        0     0     0     0     0      0
        MBTPS1 MCM3 MCOLN1 ME2 MEF2C MELK MEST METRN MFSD10 MICALL1 MIF MKNK1 MLEC MLLT11 MMP1 MMP2 MNAT1 MOK MPZL1 MRPL12 MRPL19 MRPS16 MRPS2 MSH6
10-DEBC      0    0      0   0     0    0    0     0      0       0   0     0    0      0    0    0     0   0     0      0      0      0     0    0
        MSRA MTA1 MTF2 MTFR1 MTHFD2 MUC1 MVP MYBL2 MYC MYCBP MYCBP2 MYL9 MYLK MYO10 NARFL NCAPD2 NCK1 NCK2 NCOA3 NENF NET1 NFATC3 NFATC4 NFE2L2 NFIL3
10-DEBC    0    0    0     0      0    0   0     0   0     0      0    0    0    -4     0      0    0    0     0    0    0      0      0      0     0
        NFKB2 NFKBIA NFKBIB NFKBIE NGRN NIPSNAP1 NISCH NIT1 NMT1 NNT NOL3 NOLC1 NOS3 NOSIP NOTCH1 NPC1 NPDC1 NPEPL1 NPRL2 NR1H2 NR2F6 NR3C1 NRAS
10-DEBC     0      0     -3      0    0        0     0    0    0   0    0     0    0     0      0    0     0      0     0     0     0     0    0
        NRIP1 NSDHL NT5DC2 NUCB2 NUDCD3 NUDT9 NUP133 NUP62 NUP85 NUP88 NUP93 NUSAP1 NVL ORC1 OXA1L OXCT1 OXSR1 P4HA2 P4HTM PACSIN3 PAF1 PAFAH1B1
10-DEBC     0     0      0     0      0     0      0     0     0     0     0      0   0    0     0     0     0     0     0       0    0        0
        PAFAH1B3 PAICS PAK1 PAK4 PAK6 PAN2 PAPD7 PARP1 PARP2 PAX8 PCBD1 PCCB PCK2 PCM1 PCMT1 PCNA PDGFA PDHX PDIA5 PDLIM1 PDS5A PECR PEX11A PFKL
10-DEBC        0     0    0    0    0    0     0     0     0    0     0    0    0    0     0    0     0   -3     0      0     0    0      0    0
        PGAM1 PGM1 PGRMC1 PHGDH PHKA1 PHKB PHKG2 PIGB PIH1D1 PIK3C2B PIK3C3 PIK3CA PIK3R3 PIK3R4 PIN1 PIP4K2B PKIG PLA2G15 PLA2G4A PLCB3 PLEKHJ1
10-DEBC     0    0      0     0     0    0     0    0      0       0      0      0      0      0    0       0    0       0       0     0       0
        PLEKHM1 PLK1 PLOD3 PLP2 PLS1 PLSCR1 PLSCR3 PMAIP1 PMM2 PNKP PNP POLB POLD4 POLE2 POLG2 POLR1C POLR2I POLR2K POP4 PPARD PPARG PPIC PPIE PPOX
10-DEBC       0    0     0    0    0      0      0      0    0    0   0    0     0     3     0      0      0      3    0     0     0    3    0    0
        PPP1R13B PPP2R3C PPP2R5A PPP2R5E PRAF2 PRCP PRKACA PRKAG2 PRKCD PRKCH PRKCQ PRKX PROS1 PRPF4 PRR15L PRR7 PRSS23 PRUNE PSIP1 PSMB10 PSMB8
10-DEBC        0       0       0       0     0    0      0      0    -4     0     0    0     0     0      0    0      0     0     0      0     0
        PSMD10 PSMD2 PSMD4 PSMD9 PSME1 PSME2 PSMF1 PSMG1 PSRC1 PTGS2 PTK2 PTK2B PTPN1 PTPN12 PTPN6 PTPRC PTPRF PTPRK PUF60 PWP1 PXMP2 PXN PYCR1 PYGL
10-DEBC      0     0     0     0     0     0     0     0     0     0    0     0     0      0     0     0     0     0     0    0     0   0    -3    0
        RAB11FIP2 RAB21 RAB27A RAB31 RAB4A RAC2 RAD51C RAD9A RAE1 RAI14 RALA RALB RALGDS RAP1GAP RASA1 RB1 RBKS RBM15B RBM34 RBM6 REEP5 RELB RFC2
10-DEBC        -3     0      0     0     0    0      0     0    0     0    0    0      0       0     0   0   -3      0     0   -5     0    0    0
        RFC5 RFNG RFX5 RGS2 RHEB RHOA RNF167 RNH1 RNMT RNPS1 RPA1 RPA2 RPA3 RPIA RPL39L RPN1 RPP38 RPS5 RPS6 RPS6KA1 RRAGA RRP12 RRP1B RRP8 RRS1 RSU1
10-DEBC    0    0    0    0    0    0      0    0    0     0    0    0    0    0      0    0     0    0    0       0     0     0     0    0    0    0
        RTN2 RUVBL1 S100A13 S100A4 SACM1L SATB1 SCAND1 SCARB1 SCCPDH SCP2 SCRN1 SCYL3 SDHB SENP6 SERPINE1 SESN1 SFN SGCB SH3BP5 SHB SHC1 SIRT3 SKIV2L
10-DEBC    0      0       0      0      0     0      0      0      0    0     0     0    0     0        0     0   0    0      0   0    0     0     -3
        SKP1 SLC11A2 SLC1A4 SLC25A13 SLC25A14 SLC25A4 SLC25A46 SLC27A3 SLC2A6 SLC35A1 SLC35A3 SLC35B1 SLC35F2 SLC37A4 SLC5A6 SMAD3 SMARCA4 SMARCC1
10-DEBC    0       0      0        0        0       0        0       0      0       0       0       0       0       0      0     0      -3       0
        SMARCD2 SMC1A SMC3 SMC4 SMNDC1 SNAP25 SNCA SNX11 SNX13 SNX6 SNX7 SOCS2 SORBS3 SOX2 SOX4 SPAG4 SPAG7 SPDEF SPEN SPP1 SPR SPRED2 SPTAN1 SPTLC2
10-DEBC       0     0    0    0      0      0    0     0     0    0    0     0      0    0    0     0     0     0   -4    0   0      0      0      0
        SQRDL SQSTM1 SRC SSBP2 ST3GAL5 ST6GALNAC2 ST7 STAMBP STAP2 STAT1 STAT3 STAT5B STK10 STK25 STMN1 STUB1 STX1A STX4 STXBP1 STXBP2 SUPV3L1
10-DEBC     4      0   0     0       0          0   0      0     0     0     0      0     0     0     0     0    -3    0      0      0       0
        SUV39H1 SUZ12 SYK SYNE2 SYNGR3 SYPL1 TARBP1 TATDN2 TBC1D9B TBP TBPL1 TBX2 TBXA2R TCEA2 TCEAL4 TCERG1 TCFL5 TCTA TCTN1 TERF2IP TERT TES TESK1
10-DEBC       0     0   0     0      0     0      0     -3       0   0     0    0      0     0      0     -4     0    0     0       0    0   0     0
        TEX10 TFAP2A TFDP1 TGFB3 TGFBR2 THAP11 TIAM1 TICAM1 TIMELESS TIMM17B TIMM22 TIMM9 TIMP2 TIPARP TJP1 TLE1 TLK2 TLR4 TM9SF2 TM9SF3 TMCO1 TMED10
10-DEBC     0      0     0     0      0      0     0      0        0       0      0     0     0      0    0    0    0    0      0      0     0      0
        TMEM109 TMEM110 TMEM2 TMEM5 TMEM50A TMEM97 TNFRSF21 TNIP1 TOMM34 TOMM70A TOP2A TOPBP1 TOR1A TP53 TP53BP1 TP53BP2 TPD52L2 TPM1 TRAK2 TRAM2
10-DEBC       0       0     0     0       0      0        0     0      0       0     0      0     0    0       0       0       0    0     0     0
        TRAP1 TRAPPC3 TRAPPC6A TRIB1 TRIB3 TRIM13 TRIM2 TSC22D3 TSEN2 TSKU TSPAN3 TSPAN4 TSPAN6 TSTA3 TUBB6 TWF2 TXLNA TXNDC9 TXNL4B TXNRD1 UBE2A
10-DEBC     0       0        0     0     0      0     0       0     0    0      0      0      3     0     0    0     0      0      0     -4     0
        UBE2C UBE2J1 UBE2L6 UBE3B UBE3C UBQLN2 UBR7 UFM1 UGDH USP1 USP14 USP22 USP6NL USP7 UTP14A VAPB VAT1 VAV3 VDAC1 VGLL4 VPS28 VPS72 WASF3 WDR61
10-DEBC     0      0      0     0     0      3    0    0    0    0     0     0      0    0      0    0    0    0     0     0     0     3     0     0
        WDR7 WDTC1 WFS1 WIPF2 WRB XBP1 XPNPEP1 XPO7 YKT6 YME1L1 YTHDF1 ZDHHC6 ZFP36 ZMIZ1 ZMYM2 ZNF131 ZNF274 ZNF318 ZNF395 ZNF451 ZNF586 ZNF589 ZW10
10-DEBC    0     0    0     0   0    0       0    0    0      0      0      0     0     0     0      0      0      0      0      0      0      0    0
 [ reached 'max' / getOption("max.print") -- omitted 5 rows ]
target_compound <- "triptolide"
compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, compound_sig$triptolide != 0)
data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data
     ABCF1      ABCF3      ABHD6       ABL1      ACAA1      ACBD3        ACD       ACLY      ACOT9     ADAM10      ADAT1      ADCK3       ADH5 
         7         -6          7         -4          4         -7          5         -6         -7         -5          7         -3         -3 
      ADI1        ADO        AGL      AKAP8     AKAP8L      ALAS1    ALDH7A1      ALDOC     AMDHD2      ANO10      ANXA7      APBB2       APOE 
         3         -7          5         -6          7          6          7          5          4          5         -5          6          6 
    APPBP2     ARFIP2    ARHGAP1   ARHGEF12    ARHGEF2     ARID4B     ARID5B      ARL4C      ARNT2     ARPP19      ASAH1      ASCC3       ATF1 
         3         -6          4         -5         -7         -3          3          5          7         -5          3         -5         -7 
      ATF5       ATG3      ATMIN     ATP11B     ATP1B1     ATP2C1      ATP5S    ATP6V0B      AURKA      AURKB      BACE2        BAD       BAG3 
        -3         -7         -5          7         -7          3         -5          4         -7          6          6          4         -6 
     BAMBI        BAX       BCL2      BCL7B    BHLHE40        BID      BIRC2      BLCAP       BLMH      BLVRA       BMP4      BNIP3     BNIP3L 
         5          6          6         -7         -5          6         -6         -3         -4         -5          6         -4         -6 
      BPHL      BRCA1        BTK      BUB1B      C2CD2     C2CD2L         C5      CAB39      CALM3       CALU    CAMSAP2      CANT1      CASC3 
         4         -7          6          7          3          7          7         -6          7          3          6         -5         -5 
      CASK     CASP10      CASP2      CASP3      CASP7       CAST        CAT       CBLB       CBR1       CBR3     CCDC92       CCL2      CCNA1 
        -5          7         -5          4         -6          7          6          6          3         -3          3          3          5 
     CCNA2      CCNB1      CCNB2      CCND3       CCNF       CCNH     CCP110      CD320       CD40       CD44      CDC20     CDC25A     CDC25B 
        -7         -6         -7          3         -7          3         -6          5          7          7         -7         -7         -6 
     CDC42      CDC45      CDCA4       CDH3       CDK1      CDK19       CDK4     CDK5R1       CDK7     CDKN1B     CDKN2A      CEBPD      CEBPZ 
        -6          7         -7          5         -5         -4         -6          5         -7         -6          3          7         -5 
     CENPE       CERK     CGRRF1      CHAC1      CHEK1      CHEK2      CHERP      CHIC2      CHMP6       CHN1      CLIC4       CLPX       CLTB 
        -3          7         -6          7         -4         -7         -5         -3          6          4         -6         -7          6 
      CLTC      CNDP2      CNOT4      CNPY3       COG4       COG7     COL1A1      COPB2     COPS7A     CORO1A      CPNE3      CPSF4      CREG1 
        -7         -4         -7          5          7          7          4         -3          6          4         -4          6          3 
    CRELD2        CRK       CRKL      CRTAP       CRYZ        CSK    CSNK1A1     CSNK1E    CSNK2A2      CSRP1     CTNND1       CTSD      CXCR4 
         7         -3          5          3         -4         -4         -4          6          7         -4          7          7          5 
      CYCS      CYTH1       DAXX        DCK    DCUN1D4       DDB2       DDR1      DDX10      DDX42      DECR1       DFFA       DFFB      DHDDS 
         5          4          7         -7          3         -6          6         -7         -7          6          7          6          7 
     DHRS7      DHX29        DLD      DMTF1     DNAJA3     DNAJB1     DNAJB6       DNM1      DNMT1    DNTTIP2       DPH2     DUSP11     DUSP14 
        -3         -4         -3          4          6         -7          6          4          6         -3         -3          7         -3 
     DYRK3       E2F2       EAPP   EBNA1BP2        EBP        ECD       ECH1      EDEM1       EDN1        EED        EGF       EGFR     EIF4G1 
         7          7         -6         -4         -4         -5          6          5          7         -6          6         -6          4 
      EIF5      ELAC2     ELOVL6       EML3     ENOPH1      EPHA3      EPHB2       EPN2       EPRS      ERBB2       ETS1        EVL       EXT1 
        -5          3         -5          7         -7          3          5          6         -6         -7          7          4          7 
      EZH2        FAH       FAIM     FAM20B     FAM57A     FAM63A     FAM69A        FAS    FASTKD5     FBXL12     FBXO11     FBXO21      FBXO7 
        -6          7          5          4         -5          5          6         -3         -6          6         -5          3         -5 
     FCHO1      FDFT1       FEZ2      FGFR2      FGFR4       FHL2     FKBP14      FKBP4        FOS      FOSL1      FOXJ3      FOXO3      FOXO4 
         6         -4         -3          7          7         -6          3          6          7         -3         -5         -4         -3 
      FRS2       FSD1       FUT1       FZD1       FZD7      G3BP1        GAA     GABPB1    GADD45A    GADD45B       GALE      GAPDH      GDPD5 
         7          7          7          7         -6         -5          4         -7          7          3         -7         -3          7 
     GFOD1       GLI2      GLOD4       GLRX       GMNN      GNA11      GNA15       GNAS       GNB5     GOLT1B    GPATCH8       GPC1       GRB7 
         7          6         -7         -7          6         -4          7         -4          7         -4         -7          7          7 
       GRN      GRWD1      GSTM2      GSTZ1     GTF2A2     GTF2E2     GTPBP8      H2AFV       HAT1      HDAC2     HEATR1      HERC6      HIF1A 
         5         -6          5          3         -4         -7         -6          7          3         -7         -6          4         -5 
 HIST1H2BK  HIST2H2BE        HK1      HMGCR     HMGCS1      HMOX1       HN1L     HOMER2      HOOK2     HOXA10      HOXA5     HS2ST1     HSPA1A 
         3          7         -5          5         -7         -5         -4          6          3         -5         -3          5         -5 
     HSPA4      HSPA8      HSPD1    HTATSF1      HTRA1      HYOU1      IARS2      ICAM1      ICAM3        ID2        IDE       IER3     IFNAR1 
         7         -7         -3          7          7          5         -5          6         -5         -3         -3         -4          7 
     IFRD2      IGF1R    IGF2BP2      IGF2R     IGFBP3    IGHMBP2     IKBKAP      IKBKB      IKBKE      IKZF1    IL13RA1       IL1B       IL4R 
        -3         -4         -4          7          6          5         -6          7          6          7          7          6          7 
     INPP1     INPP4B     INSIG1      INTS3      IPO13     IQGAP1      ISOC1      ITFG1      ITGAE      ITGB5      JMJD6        JUN      KAT6A 
        -5         -5         -3         -6          7          7          5          7          5          3         -6          5         -4 
     KCNK1      KCTD5      KDM3A      KDM5A      KDM5B   KIAA0196   KIAA0355   KIAA0753   KIAA0907   KIAA1033      KIF14     KIF20A      KIF2C 
        -4          6         -7         -6          3          6          4          6         -3         -7         -6         -7         -6 
     KIF5C        KIT      LAGE3       LAP3        LBR     LGALS8       LGMN      LOXL1      LPAR2     LPGAT1     LRPAP1       LSM5       LSM6 
        -6          7          3          6         -7          7          7          3          4         -6          6         -3         -5 
       LSR        LYN     LYPLA1      MACF1     MAN2B1     MAP2K5     MAP3K4     MAP4K4  MAPK1IP1L      MAPK9   MAPKAPK2   MAPKAPK3   MAPKAPK5 
         7          6         -5         -7          7          5         -7         -5         -7          6         -3          3         -4 
     MAT2A      MBNL1      MBNL2     MBTPS1       MCM3     MCOLN1       MELK       MEST    MICALL1      MKNK1       MMP1       MMP2      MNAT1 
        -7         -7         -7          6         -7          7         -4          7         -7          6          6          6         -6 
     MPZL1     MRPL12     MRPL19     MRPS16      MRPS2       MSH6       MSRA       MTA1       MTF2      MTFR1     MTHFD2        MVP      MYBL2 
        -6         -7         -3         -6         -7         -7          5          3         -7          6         -7          7          7 
       MYC     MYCBP2       MYL9      MYO10      NARFL     NCAPD2       NCK1       NCK2      NCOA3       NENF       NET1     NFATC4     NFE2L2 
        -5          4          6         -4          7          4         -7         -5          4          5         -4          7          6 
     NFKB2     NFKBIA     NFKBIB     NFKBIE       NGRN      NISCH       NIT1       NOL3      NOLC1       NOS3     NOTCH1       NPC1      NPDC1 
         4         -7          6          7          7          4          7          6         -5          5          7         -4          6 
    NPEPL1      NPRL2      NR1H2      NR2F6      NRIP1      NSDHL     NT5DC2      NUCB2     NUDCD3      NUDT9      NUP62      NUP85      NUP88 
         5          5          5         -4         -7         -4          6          4         -3         -6         -7         -7         -6 
    NUSAP1        NVL       ORC1      OXA1L      OXCT1      OXSR1      P4HTM       PAF1   PAFAH1B1      PAICS      PAPD7      PARP2       PAX8 
        -6          7          7         -5          5         -6          6          7          7         -5          6         -7          5 
      PCCB       PCK2       PCM1      PCMT1       PCNA      PDGFA       PDHX     PDLIM1      PDS5A       PECR       PFKL       PGM1      PHKA1 
         3          6         -7         -6         -7         -7         -6          4         -5          6          5         -3          5 
      PHKB      PHKG2     PIH1D1    PIK3C2B     PIK3CA     PIK3R3     PIK3R4    PIP4K2B    PLA2G4A      PLCB3    PLEKHM1       PLK1      PLOD3 
         7          6          6         -4          6          3         -5         -6          7          5          7         -7          5 
      PLP2       PLS1     PMAIP1       PMM2        PNP      POLD4      POLE2      POLG2     POLR1C     POLR2K       POP4      PPARD       PPOX 
         7          3          7          6         -4         -4         -7         -4          3         -4         -7          7          7 
  PPP1R13B    PPP2R3C    PPP2R5E       PRCP     PRKACA      PRKCQ       PRKX      PROS1      PRPF4     PRR15L       PRR7     PRSS23      PRUNE 
         7         -6          4          6          6          7          7          3         -6          7          6         -3         -3 
     PSIP1     PSMB10      PSMB8     PSMD10      PSMD2      PSMD4      PSMD9      PSMF1      PSMG1      PSRC1      PTGS2       PTK2      PTK2B 
        -5          4         -3         -6          6         -4          4          7         -7         -4          5         -5          7 
     PTPN1     PTPN12      PTPRC      PTPRF      PTPRK      PUF60       PWP1        PXN      RAB21     RAB27A      RAB31      RAB4A       RAC2 
         5         -6          7          7          6         -7         -7          7          7          4          5         -5          4 
    RAD51C      RAD9A       RAE1      RAI14       RALA       RALB    RAP1GAP      RASA1       RBKS     RBM15B      RBM34       RBM6       RFNG 
         4         -5         -7          7          3         -6          4         -3          3          5         -5          3          6 
      RFX5       RGS2       RHEB       RNH1       RNMT      RNPS1       RPA2       RPA3     RPL39L      RPP38       RPS5       RPS6      RRAGA 
        -5         -4         -7          7         -7         -6          5         -5         -3         -7          3         -5         -4 
     RRP12      RRP1B       RRP8       RSU1       RTN2     RUVBL1     SACM1L     SCAND1     SCARB1     SCCPDH       SCP2      SCYL3       SDHB 
         6         -7         -3          4          7          6         -6         -6          7         -4          5         -6         -3 
     SENP6   SERPINE1        SFN       SGCB        SHB       SHC1      SIRT3    SLC11A2   SLC25A13   SLC25A46    SLC27A3     SLC2A6    SLC35A3 
        -7          6         -3          3          6          4          5          5         -5         -6          6         -3         -3 
   SLC35B1    SLC35F2    SLC37A4     SLC5A6      SMAD3    SMARCA4    SMARCC1       SMC3       SMC4     SMNDC1     SNAP25       SNCA      SNX11 
        -4         -7         -6          3         -6         -5         -5         -4         -7         -5          6          5         -7 
     SNX13       SNX7      SOCS2       SOX2       SOX4      SPAG4      SPAG7      SPDEF       SPEN        SPR     SPRED2     SPTAN1     SPTLC2 
         6          7          7          7         -5          4          7          3         -6         -4          7         -3         -6 
     SQRDL     SQSTM1        SRC      SSBP2    ST3GAL5 ST6GALNAC2        ST7     STAMBP      STAP2     STAT5B      STK10      STUB1       STX4 
         4         -6         -3          6          5          3         -7         -7          7          5          7         -3          7 
    STXBP1     STXBP2    SUPV3L1    SUV39H1      SUZ12        SYK      SYNE2      SYPL1     TARBP1     TATDN2        TBP      TBPL1       TBX2 
        -5          5          7         -7         -7          5         -4         -3          6         -6         -7         -4          4 
    TBXA2R      TCEA2     TCERG1       TCTA      TCTN1    TERF2IP       TERT        TES      TESK1     TFAP2A      TGFB3     TGFBR2     THAP11 
         6          7         -7          3          5         -5          7          4          7          7          7         -6         -4 
    TICAM1   TIMELESS    TIMM17B     TIMM22      TIMM9      TIMP2     TIPARP       TJP1       TLE1       TLR4     TM9SF2     TMED10    TMEM110 
         3          3         -4          7         -7          7          3         -4         -6         -4         -6          4          7 
     TMEM2      TMEM5    TMEM50A     TMEM97    TOMM70A      TOP2A      TOR1A    TP53BP1    TP53BP2    TPD52L2       TPM1      TRAK2      TRAM2 
        -5         -5         -3         -7         -7         -7          5         -4          4          6         -4         -7         -4 
     TRAP1    TRAPPC3   TRAPPC6A      TRIB3     TRIM13      TRIM2      TSEN2       TSKU      TUBB6       TWF2      TXLNA     TXNDC9     TXNRD1 
         7         -7          7          4          7          5         -3         -5         -3         -5         -7         -4         -6 
     UBE2C     UBE2J1     UBE2L6      UBE3B       UBR7       USP1      USP14      USP22     USP6NL       USP7       VAT1       VAV3      VDAC1 
        -7          7          6          7         -3         -6          3         -7         -6         -7         -3          6         -4 
     VGLL4      VPS28      VPS72      WASF3      WDR61       WDR7      WIPF2        WRB       XBP1    XPNPEP1       XPO7       YKT6     YTHDF1 
        -5         -6          4          4         -6          7         -4         -4         -6         -3         -6         -7         -6 
    ZDHHC6      ZFP36      ZMYM2     ZNF131     ZNF395     ZNF589       ZW10 
        -4          3         -6         -7          7          6         -4 
barplot(data, horiz = TRUE, col = "red")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
pdf(file = "triptolide_sig_heatmap.pdf")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()
pdf 
  3 

So now subset this signature for genes within different medulloblastoma disease signatures. A good way to pick which one is ideal is to find which one this drug reverses the disease signature most of.

So let’s load in the medulloblastoma disease signature data from Anna. - This is a microarray dataset, so some genes have multiple probes. These probes are labeled for specificity, but for this purpose we will just average duplicate rows, so each gene’s reported fold-change is representative of all probes for each gene.

First, we should subset columns that are averagable.. ie. numeric So Fold-change.

Then we will avverage the fold changes within each gene, and use that to calculate signature overlap with compound response signatures.

library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union
MedulloSigs <- read.csv(file = "MedulloSigs.csv", skip = 1, header = TRUE)
head(MedulloSigs)
          X       G4     G4.1     G4.2     G4.3     G4.4     G4.5     G4.6     G4.7     G4.8     G4.9    G4.10    G4.11    G4.12    G4.13    G4.14
1 1007_s_at 7.595940 7.806655 7.401414 7.603100 7.996856 7.825205 7.683266 7.457205 7.562213 7.349231 7.692980 6.847049 6.988782 7.347686 7.491087
2   1053_at 6.144400 6.191544 5.907811 6.052795 6.883360 6.283014 5.882486 6.577583 5.841223 6.801283 6.385026 6.321308 6.137943 6.116995 6.906354
3    117_at 4.824306 5.244389 4.805659 4.051785 4.535820 4.763028 4.822698 3.484312 4.938065 4.363099 5.048573 4.287716 4.467057 3.517498 4.783316
4    121_at 5.670915 5.621487 5.978379 5.599533 5.769882 5.278115 5.732694 5.846439 5.827768 5.992464 5.660527 5.930387 5.950121 5.687315 6.205769
5 1255_g_at 4.141546 3.417727 4.218036 3.653252 3.535145 3.683867 3.781914 3.970292 3.443618 3.384390 3.718438 4.067316 3.975936 5.742682 6.078101
6   1294_at 5.489351 5.704782 5.436774 5.157905 5.551020 5.652489 5.562603 4.999911 5.572154 5.659134 5.755425 5.354698 5.767070 5.429784 5.430661
     G4.15    G4.16    G4.17    G4.18    G4.19    G4.20    G4.21    G4.22    G4.23    G4.24    G4.25    G4.26    G4.27    G4.28    G4.29    G4.30
1 7.481837 7.670195 7.220520 7.658086 7.767983 6.940416 7.127614 6.386037 7.178317 7.387895 7.024382 7.156177 7.432957 6.742055 7.073693 7.285918
2 6.583686 6.274951 6.270232 6.959778 6.529857 6.283947 6.006599 6.608406 5.874931 6.296741 6.148041 6.606785 5.929855 6.291013 7.048820 6.531606
3 4.784153 4.865224 3.811097 4.720283 5.874088 4.608166 4.804021 4.255613 5.142832 5.258536 4.741448 4.440296 3.605498 3.600048 3.916015 4.422449
4 5.967428 5.742362 5.824524 5.388158 6.076265 6.026107 5.838604 5.771130 5.280153 5.179534 5.875493 5.623295 5.231109 5.210578 5.786283 5.412539
5 4.560173 4.671894 3.377588 4.782479 4.383276 4.953712 4.062166 5.261653 4.169761 7.480992 4.993150 4.371976 3.214868 5.308268 4.345103 4.618086
6 5.176150 5.137562 5.019925 5.267858 5.007965 5.054333 5.605802 5.013963 5.152135 5.991465 5.282188 4.852030 5.077047 5.295313 5.063860 5.064492
     G4.31    G4.32    G4.33    G4.34    G4.35    G4.36    G4.37    G4.38       G3     G3.1     G3.2     G3.3     G3.4     G3.5     G3.6     G3.7
1 6.946303 7.805026 7.751303 7.649788 7.330798 7.500640 7.667673 7.757735 7.792349 8.260027 7.332892 7.128977 6.899421 6.170656 7.302496 7.727711
2 6.224955 6.617671 6.372637 6.606785 5.766757 6.388730 6.606110 6.893149 6.579529 7.080868 6.642747 6.012002 6.596873 6.690097 6.358189 6.204356
3 4.999911 4.498698 3.317816 3.613617 4.067316 4.136765 4.429626 3.756538 4.907495 5.773620 6.098074 4.794964 4.833898 5.285232 4.154184 4.415220
4 5.220356 5.660875 5.980151 5.861640 5.938591 5.984188 5.436774 6.090857 6.212406 6.282827 6.110358 5.918625 6.018593 5.894954 5.746522 6.061457
5 3.462606 4.652054 5.874650 4.259859 3.912023 4.172848 4.930871 3.676301 3.152736 3.404525 4.483003 6.736730 4.616110 3.616309 5.146913 6.079933
6 4.762174 4.976734 5.428029 5.705115 5.177279 4.112512 5.232178 5.925859 5.472691 6.110802 5.416989 4.933034 5.138149 5.334167 4.807294 4.941642
      G3.8     G3.9    G3.10    G3.11    G3.12    G3.13    G3.14    G3.15      WNT    WNT.1    WNT.2    WNT.3    WNT.4    WNT.5    WNT.6    WNT.7
1 7.287560 6.780603 7.560757 6.719979 7.536524 6.942350 7.408894 6.756235 7.600802 7.725507 6.760878 7.165107 6.799502 7.647977 6.919091 6.641443
2 6.734591 6.830982 6.795929 7.313420 6.337003 6.025624 6.564560 6.335409 5.974064 6.624198 6.735305 6.163946 6.448573 6.202940 6.602316 6.553648
3 5.101694 4.949469 5.183467 4.417635 3.508556 4.530447 5.073297 3.992681 5.362700 4.853591 4.325456 5.057519 3.610918 4.461300 4.130355 4.306764
4 5.905362 5.780435 5.378514 5.666773 5.862210 5.369708 5.897429 5.580861 5.785977 5.922650 5.800607 5.441985 5.772686 5.318610 5.808143 5.411200
5 6.037632 5.415656 5.078294 3.921973 6.176075 4.332048 5.868732 5.468060 3.328627 3.779634 3.214868 4.301359 3.713572 3.218876 3.716008 5.013963
6 5.252274 4.420045 4.989071 5.109575 4.703204 5.046646 5.066385 5.382199 6.133398 4.886583 5.068904 4.864453 5.165357 5.551796 4.950177 4.668145
       SHH    SHH.1    SHH.2    SHH.3    SHH.4    SHH.5    SHH.6    SHH.7    SHH.8    SHH.9 MEDIAN_OVERALL MEDIAN_G4 MEDIAN_G3 MEDIAN_WNT MEDIAN_SHH
1 7.545496 7.937874 7.673595 6.877605 6.945340 7.776745 7.462502 7.460433 7.466914 7.750744       7.432957  7.457205  7.295028   7.042099   7.506205
2 6.178773 6.507725 6.100991 6.377067 6.315358 6.776963 6.173369 6.482343 6.058188 6.541607       6.377067  6.296741  6.588201   6.501111   6.346213
3 5.790877 4.588024 4.453184 4.797442 4.725616 4.714921 4.445002 5.213848 4.563306 4.163559       4.588024  4.498698  4.870697   4.393378   4.651472
4 6.218002 5.592478 5.796361 6.023205 5.615680 5.797880 5.792709 5.859931 5.993961 6.115450       5.797880  5.771130  5.896191   5.779331   5.828906
5 4.614130 4.025352 3.962716 3.487375 3.246491 4.584968 4.338597 3.532226 4.599152 4.044804       4.218036  4.172848  5.112603   3.714790   4.035078
6 5.677096 5.467638 5.564137 5.925325 5.566434 5.626901 5.357529 5.349961 5.822750 5.554121       5.282188  5.282188  5.087980   5.009540   5.565285
     Log2FC_G4   Log2FC_G3   Log2FC_WNT   Log2FC_SHH X.1 Probe.Set.ID Gene.Symbol  X.2 X.3 X.4 X.5 X.6 X.7
1  0.004698740 -0.02702275 -0.077930753  0.014147430  NA    1007_s_at        DDR1 TRUE  NA  NA  NA  NA  NA
2 -0.018287712  0.04699153  0.027793137 -0.006997209  NA      1053_at        RFC2 TRUE  NA  NA  NA  NA  NA
3 -0.028365417  0.08625515 -0.062542306  0.019814559  NA       117_at       HSPA6 TRUE  NA  NA  NA  NA  NA
4 -0.006671645  0.02425791 -0.004622849  0.007699538  NA       121_at        PAX8 TRUE  NA  NA  NA  NA  NA
5 -0.015539038  0.27748674 -0.183290752 -0.063974847  NA    1255_g_at      GUCA1A TRUE  NA  NA  NA  NA  NA
6  0.000000000 -0.05404265 -0.076457372  0.075320050  NA      1294_at        UBA7 TRUE  NA  NA  NA  NA  NA
myvars <- c("Gene.Symbol", "Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat <- MedulloSigs[myvars]
myvars2 <- c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct
funs() is soft deprecated as of dplyr 0.8.0
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once per session.
head(dat2)
rownames(dat2) <- dat2$Gene.Symbol
Setting row names on a tibble is deprecated.
MedulloSigs <- dat2
rm(dat)
rm(dat2)

Now, let’s subset this medullo data for the genes that are in the compound response signature. Then, we can assess differential discordance.

head(MedulloSigs)
head(compound_sig)
      triptolide
ABCF1          7
ABCF3         -6
ABHD6          7
ABL1          -4
ACAA1          4
ACBD3         -7
cmpdGenes <- rownames(compound_sig)
  # obj.transpose <- t(obj@assays$SCT@scale.data) 
  cmpd_overlap <- rownames(MedulloSigs)[which(rownames(MedulloSigs) %in% cmpdGenes)]
  overlap <- MedulloSigs[cmpd_overlap,] # FileA
  overlap
  rownames(overlap) <- overlap$Gene.Symbol
Setting row names on a tibble is deprecated.
  
  # overlap$Gene.Symbol <- NULL
  head(overlap)
  
  cmpd_ordered <- as.numeric(as.vector(t(compound_sig)))
  names(cmpd_ordered) <- rownames(compound_sig)
  cmpd_ordered
     ABCF1      ABCF3      ABHD6       ABL1      ACAA1      ACBD3        ACD       ACLY      ACOT9     ADAM10      ADAT1      ADCK3       ADH5 
         7         -6          7         -4          4         -7          5         -6         -7         -5          7         -3         -3 
      ADI1        ADO        AGL      AKAP8     AKAP8L      ALAS1    ALDH7A1      ALDOC     AMDHD2      ANO10      ANXA7      APBB2       APOE 
         3         -7          5         -6          7          6          7          5          4          5         -5          6          6 
    APPBP2     ARFIP2    ARHGAP1   ARHGEF12    ARHGEF2     ARID4B     ARID5B      ARL4C      ARNT2     ARPP19      ASAH1      ASCC3       ATF1 
         3         -6          4         -5         -7         -3          3          5          7         -5          3         -5         -7 
      ATF5       ATG3      ATMIN     ATP11B     ATP1B1     ATP2C1      ATP5S    ATP6V0B      AURKA      AURKB      BACE2        BAD       BAG3 
        -3         -7         -5          7         -7          3         -5          4         -7          6          6          4         -6 
     BAMBI        BAX       BCL2      BCL7B    BHLHE40        BID      BIRC2      BLCAP       BLMH      BLVRA       BMP4      BNIP3     BNIP3L 
         5          6          6         -7         -5          6         -6         -3         -4         -5          6         -4         -6 
      BPHL      BRCA1        BTK      BUB1B      C2CD2     C2CD2L         C5      CAB39      CALM3       CALU    CAMSAP2      CANT1      CASC3 
         4         -7          6          7          3          7          7         -6          7          3          6         -5         -5 
      CASK     CASP10      CASP2      CASP3      CASP7       CAST        CAT       CBLB       CBR1       CBR3     CCDC92       CCL2      CCNA1 
        -5          7         -5          4         -6          7          6          6          3         -3          3          3          5 
     CCNA2      CCNB1      CCNB2      CCND3       CCNF       CCNH     CCP110      CD320       CD40       CD44      CDC20     CDC25A     CDC25B 
        -7         -6         -7          3         -7          3         -6          5          7          7         -7         -7         -6 
     CDC42      CDC45      CDCA4       CDH3       CDK1      CDK19       CDK4     CDK5R1       CDK7     CDKN1B     CDKN2A      CEBPD      CEBPZ 
        -6          7         -7          5         -5         -4         -6          5         -7         -6          3          7         -5 
     CENPE       CERK     CGRRF1      CHAC1      CHEK1      CHEK2      CHERP      CHIC2      CHMP6       CHN1      CLIC4       CLPX       CLTB 
        -3          7         -6          7         -4         -7         -5         -3          6          4         -6         -7          6 
      CLTC      CNDP2      CNOT4      CNPY3       COG4       COG7     COL1A1      COPB2     COPS7A     CORO1A      CPNE3      CPSF4      CREG1 
        -7         -4         -7          5          7          7          4         -3          6          4         -4          6          3 
    CRELD2        CRK       CRKL      CRTAP       CRYZ        CSK    CSNK1A1     CSNK1E    CSNK2A2      CSRP1     CTNND1       CTSD      CXCR4 
         7         -3          5          3         -4         -4         -4          6          7         -4          7          7          5 
      CYCS      CYTH1       DAXX        DCK    DCUN1D4       DDB2       DDR1      DDX10      DDX42      DECR1       DFFA       DFFB      DHDDS 
         5          4          7         -7          3         -6          6         -7         -7          6          7          6          7 
     DHRS7      DHX29        DLD      DMTF1     DNAJA3     DNAJB1     DNAJB6       DNM1      DNMT1    DNTTIP2       DPH2     DUSP11     DUSP14 
        -3         -4         -3          4          6         -7          6          4          6         -3         -3          7         -3 
     DYRK3       E2F2       EAPP   EBNA1BP2        EBP        ECD       ECH1      EDEM1       EDN1        EED        EGF       EGFR     EIF4G1 
         7          7         -6         -4         -4         -5          6          5          7         -6          6         -6          4 
      EIF5      ELAC2     ELOVL6       EML3     ENOPH1      EPHA3      EPHB2       EPN2       EPRS      ERBB2       ETS1        EVL       EXT1 
        -5          3         -5          7         -7          3          5          6         -6         -7          7          4          7 
      EZH2        FAH       FAIM     FAM20B     FAM57A     FAM63A     FAM69A        FAS    FASTKD5     FBXL12     FBXO11     FBXO21      FBXO7 
        -6          7          5          4         -5          5          6         -3         -6          6         -5          3         -5 
     FCHO1      FDFT1       FEZ2      FGFR2      FGFR4       FHL2     FKBP14      FKBP4        FOS      FOSL1      FOXJ3      FOXO3      FOXO4 
         6         -4         -3          7          7         -6          3          6          7         -3         -5         -4         -3 
      FRS2       FSD1       FUT1       FZD1       FZD7      G3BP1        GAA     GABPB1    GADD45A    GADD45B       GALE      GAPDH      GDPD5 
         7          7          7          7         -6         -5          4         -7          7          3         -7         -3          7 
     GFOD1       GLI2      GLOD4       GLRX       GMNN      GNA11      GNA15       GNAS       GNB5     GOLT1B    GPATCH8       GPC1       GRB7 
         7          6         -7         -7          6         -4          7         -4          7         -4         -7          7          7 
       GRN      GRWD1      GSTM2      GSTZ1     GTF2A2     GTF2E2     GTPBP8      H2AFV       HAT1      HDAC2     HEATR1      HERC6      HIF1A 
         5         -6          5          3         -4         -7         -6          7          3         -7         -6          4         -5 
 HIST1H2BK  HIST2H2BE        HK1      HMGCR     HMGCS1      HMOX1       HN1L     HOMER2      HOOK2     HOXA10      HOXA5     HS2ST1     HSPA1A 
         3          7         -5          5         -7         -5         -4          6          3         -5         -3          5         -5 
     HSPA4      HSPA8      HSPD1    HTATSF1      HTRA1      HYOU1      IARS2      ICAM1      ICAM3        ID2        IDE       IER3     IFNAR1 
         7         -7         -3          7          7          5         -5          6         -5         -3         -3         -4          7 
     IFRD2      IGF1R    IGF2BP2      IGF2R     IGFBP3    IGHMBP2     IKBKAP      IKBKB      IKBKE      IKZF1    IL13RA1       IL1B       IL4R 
        -3         -4         -4          7          6          5         -6          7          6          7          7          6          7 
     INPP1     INPP4B     INSIG1      INTS3      IPO13     IQGAP1      ISOC1      ITFG1      ITGAE      ITGB5      JMJD6        JUN      KAT6A 
        -5         -5         -3         -6          7          7          5          7          5          3         -6          5         -4 
     KCNK1      KCTD5      KDM3A      KDM5A      KDM5B   KIAA0196   KIAA0355   KIAA0753   KIAA0907   KIAA1033      KIF14     KIF20A      KIF2C 
        -4          6         -7         -6          3          6          4          6         -3         -7         -6         -7         -6 
     KIF5C        KIT      LAGE3       LAP3        LBR     LGALS8       LGMN      LOXL1      LPAR2     LPGAT1     LRPAP1       LSM5       LSM6 
        -6          7          3          6         -7          7          7          3          4         -6          6         -3         -5 
       LSR        LYN     LYPLA1      MACF1     MAN2B1     MAP2K5     MAP3K4     MAP4K4  MAPK1IP1L      MAPK9   MAPKAPK2   MAPKAPK3   MAPKAPK5 
         7          6         -5         -7          7          5         -7         -5         -7          6         -3          3         -4 
     MAT2A      MBNL1      MBNL2     MBTPS1       MCM3     MCOLN1       MELK       MEST    MICALL1      MKNK1       MMP1       MMP2      MNAT1 
        -7         -7         -7          6         -7          7         -4          7         -7          6          6          6         -6 
     MPZL1     MRPL12     MRPL19     MRPS16      MRPS2       MSH6       MSRA       MTA1       MTF2      MTFR1     MTHFD2        MVP      MYBL2 
        -6         -7         -3         -6         -7         -7          5          3         -7          6         -7          7          7 
       MYC     MYCBP2       MYL9      MYO10      NARFL     NCAPD2       NCK1       NCK2      NCOA3       NENF       NET1     NFATC4     NFE2L2 
        -5          4          6         -4          7          4         -7         -5          4          5         -4          7          6 
     NFKB2     NFKBIA     NFKBIB     NFKBIE       NGRN      NISCH       NIT1       NOL3      NOLC1       NOS3     NOTCH1       NPC1      NPDC1 
         4         -7          6          7          7          4          7          6         -5          5          7         -4          6 
    NPEPL1      NPRL2      NR1H2      NR2F6      NRIP1      NSDHL     NT5DC2      NUCB2     NUDCD3      NUDT9      NUP62      NUP85      NUP88 
         5          5          5         -4         -7         -4          6          4         -3         -6         -7         -7         -6 
    NUSAP1        NVL       ORC1      OXA1L      OXCT1      OXSR1      P4HTM       PAF1   PAFAH1B1      PAICS      PAPD7      PARP2       PAX8 
        -6          7          7         -5          5         -6          6          7          7         -5          6         -7          5 
      PCCB       PCK2       PCM1      PCMT1       PCNA      PDGFA       PDHX     PDLIM1      PDS5A       PECR       PFKL       PGM1      PHKA1 
         3          6         -7         -6         -7         -7         -6          4         -5          6          5         -3          5 
      PHKB      PHKG2     PIH1D1    PIK3C2B     PIK3CA     PIK3R3     PIK3R4    PIP4K2B    PLA2G4A      PLCB3    PLEKHM1       PLK1      PLOD3 
         7          6          6         -4          6          3         -5         -6          7          5          7         -7          5 
      PLP2       PLS1     PMAIP1       PMM2        PNP      POLD4      POLE2      POLG2     POLR1C     POLR2K       POP4      PPARD       PPOX 
         7          3          7          6         -4         -4         -7         -4          3         -4         -7          7          7 
  PPP1R13B    PPP2R3C    PPP2R5E       PRCP     PRKACA      PRKCQ       PRKX      PROS1      PRPF4     PRR15L       PRR7     PRSS23      PRUNE 
         7         -6          4          6          6          7          7          3         -6          7          6         -3         -3 
     PSIP1     PSMB10      PSMB8     PSMD10      PSMD2      PSMD4      PSMD9      PSMF1      PSMG1      PSRC1      PTGS2       PTK2      PTK2B 
        -5          4         -3         -6          6         -4          4          7         -7         -4          5         -5          7 
     PTPN1     PTPN12      PTPRC      PTPRF      PTPRK      PUF60       PWP1        PXN      RAB21     RAB27A      RAB31      RAB4A       RAC2 
         5         -6          7          7          6         -7         -7          7          7          4          5         -5          4 
    RAD51C      RAD9A       RAE1      RAI14       RALA       RALB    RAP1GAP      RASA1       RBKS     RBM15B      RBM34       RBM6       RFNG 
         4         -5         -7          7          3         -6          4         -3          3          5         -5          3          6 
      RFX5       RGS2       RHEB       RNH1       RNMT      RNPS1       RPA2       RPA3     RPL39L      RPP38       RPS5       RPS6      RRAGA 
        -5         -4         -7          7         -7         -6          5         -5         -3         -7          3         -5         -4 
     RRP12      RRP1B       RRP8       RSU1       RTN2     RUVBL1     SACM1L     SCAND1     SCARB1     SCCPDH       SCP2      SCYL3       SDHB 
         6         -7         -3          4          7          6         -6         -6          7         -4          5         -6         -3 
     SENP6   SERPINE1        SFN       SGCB        SHB       SHC1      SIRT3    SLC11A2   SLC25A13   SLC25A46    SLC27A3     SLC2A6    SLC35A3 
        -7          6         -3          3          6          4          5          5         -5         -6          6         -3         -3 
   SLC35B1    SLC35F2    SLC37A4     SLC5A6      SMAD3    SMARCA4    SMARCC1       SMC3       SMC4     SMNDC1     SNAP25       SNCA      SNX11 
        -4         -7         -6          3         -6         -5         -5         -4         -7         -5          6          5         -7 
     SNX13       SNX7      SOCS2       SOX2       SOX4      SPAG4      SPAG7      SPDEF       SPEN        SPR     SPRED2     SPTAN1     SPTLC2 
         6          7          7          7         -5          4          7          3         -6         -4          7         -3         -6 
     SQRDL     SQSTM1        SRC      SSBP2    ST3GAL5 ST6GALNAC2        ST7     STAMBP      STAP2     STAT5B      STK10      STUB1       STX4 
         4         -6         -3          6          5          3         -7         -7          7          5          7         -3          7 
    STXBP1     STXBP2    SUPV3L1    SUV39H1      SUZ12        SYK      SYNE2      SYPL1     TARBP1     TATDN2        TBP      TBPL1       TBX2 
        -5          5          7         -7         -7          5         -4         -3          6         -6         -7         -4          4 
    TBXA2R      TCEA2     TCERG1       TCTA      TCTN1    TERF2IP       TERT        TES      TESK1     TFAP2A      TGFB3     TGFBR2     THAP11 
         6          7         -7          3          5         -5          7          4          7          7          7         -6         -4 
    TICAM1   TIMELESS    TIMM17B     TIMM22      TIMM9      TIMP2     TIPARP       TJP1       TLE1       TLR4     TM9SF2     TMED10    TMEM110 
         3          3         -4          7         -7          7          3         -4         -6         -4         -6          4          7 
     TMEM2      TMEM5    TMEM50A     TMEM97    TOMM70A      TOP2A      TOR1A    TP53BP1    TP53BP2    TPD52L2       TPM1      TRAK2      TRAM2 
        -5         -5         -3         -7         -7         -7          5         -4          4          6         -4         -7         -4 
     TRAP1    TRAPPC3   TRAPPC6A      TRIB3     TRIM13      TRIM2      TSEN2       TSKU      TUBB6       TWF2      TXLNA     TXNDC9     TXNRD1 
         7         -7          7          4          7          5         -3         -5         -3         -5         -7         -4         -6 
     UBE2C     UBE2J1     UBE2L6      UBE3B       UBR7       USP1      USP14      USP22     USP6NL       USP7       VAT1       VAV3      VDAC1 
        -7          7          6          7         -3         -6          3         -7         -6         -7         -3          6         -4 
     VGLL4      VPS28      VPS72      WASF3      WDR61       WDR7      WIPF2        WRB       XBP1    XPNPEP1       XPO7       YKT6     YTHDF1 
        -5         -6          4          4         -6          7         -4         -4         -6         -3         -6         -7         -6 
    ZDHHC6      ZFP36      ZMYM2     ZNF131     ZNF395     ZNF589       ZW10 
        -4          3         -6         -7          7          6         -4 
  cmpd_ordered2 <- cmpd_ordered[cmpd_overlap] # Character list in brackets orders to fit that character list...
  
  cmpd_ordered2
      DDR1       PAX8     SCARB1      PTPRC      JMJD6       TLR4      CNPY3    PIP4K2B      SNX13      MBNL2      MYO10     TXNDC9     DNAJA3 
         6          5          7          7         -6         -4          5         -6          6         -7         -4         -4          6 
     ATP5S      CANT1       GNB5      TRAM2      FBXO7      CRTAP      GFOD1     ATP11B     PSMD10    ARHGEF2      TOR1A      PSIP1      FGFR4 
        -5         -5          7         -4         -5          3          7          7         -6         -7          5         -5          7 
     PTGS2     LPGAT1     STAT5B       TERT       ETS1      ASAH1       RNH1      TGFB3      MBNL1     CDC25A       RHEB      TRIB3    CSNK1A1 
         5         -6          5          7          7          3          7          7         -7         -7         -7          4         -4 
      SPEN     HOMER2      ITFG1      TSEN2     HEATR1      PHKG2     FAM69A     COL1A1     SNAP25       RBM6      TCTN1      BLCAP     NT5DC2 
        -6          6          7         -3         -6          6          6          4          6          3          5         -3          6 
      SMC3      KIF5C      G3BP1     MYCBP2     ZNF131        SHB       PCCB       GALE       CD44     CTNND1     ARID5B        SRC       ATF1 
        -4         -6         -5          4         -7          6          3         -7          7          7          3         -3         -7 
     SYNE2       TPM1      SSBP2     MAP4K4       NOL3       RRP8      RRP12      KAT6A       PTK2   ARHGEF12    TIMM17B      DDX42      FKBP4 
        -4         -4          6         -5          6         -3          6         -4         -5         -5         -4         -7          6 
     MKNK1      DYRK3       RSU1     TXNRD1      TXLNA      CCND3      NCOA3      CNDP2      DDX10      HERC6     INPP4B       CAST       EDN1 
         6          7          4         -6         -7          3          4         -4         -7          4         -5          7          7 
      EGFR     TATDN2     PRSS23      IKZF1      SUZ12      KCNK1       MMP2     NFE2L2       SOX4      CHERP   SERPINE1      IGF2R    SMARCA4 
        -6         -6         -3          7         -7         -4          6          6         -5         -5          6          7         -5 
   TP53BP1     TRIM13       PRCP     CCP110    PPP2R3C     STXBP2        BAD       RPS5      ABCF1      SPAG7      RNPS1     SMNDC1    ATP6V0B 
        -4          7          6         -6         -6          5          4          3          7          7         -6         -5          4 
      RPS6      USP22       CLTC      CSRP1      PTPRF     DNAJB1       XBP1        GRN        HK1       CALU       CTSD      MAT2A       GNAS 
        -5         -7         -7         -4          7         -7         -6          5         -5          3          7         -7         -4 
      ECH1     IQGAP1     HSPA1A      HSPD1   PAFAH1B1      HYOU1      PSMD2       EPRS      PSMD4     TMED10      HIF1A      PAICS      PSMF1 
         6          7         -5         -3          7          5          6         -6         -4          4         -5         -5          7 
      MYL9    SMARCC1     TM9SF2        PXN      COPB2       PFKL      ITGB5       ACLY       PLP2    BHLHE40    TERF2IP      HTRA1     LRPAP1 
         6         -5         -6          7         -3          5          3         -6          7         -5         -5          7          6 
     CREG1       PCNA       LGMN     ATP1B1      SYPL1     NUDCD3      TOP2A   EBNA1BP2       SCP2      ANXA7    TPD52L2      TRAP1        CAT 
         3         -7          7         -7         -3         -3         -7         -4          5         -5          6          7          6 
  MAPKAPK2        JUN       SHC1     SQSTM1       USP7     NFKBIA    TOMM70A      ZFP36      KDM5B       MCM3       RAE1      CLIC4        ID2 
        -3          5          4         -6         -7         -7         -7          3          3         -7         -7         -6         -3 
     NISCH       PWP1     RUVBL1     MBTPS1     INSIG1      RRAGA       IER3     UBE2L6       SMC4      USP14        PNP      DNMT1      MYBL2 
         4         -7          6          6         -3         -4         -4          6         -7          3         -4          6          7 
      RPA2     MTHFD2       DAXX      ELAC2     NCAPD2        LBR     SCCPDH       NET1      HDAC2      BNIP3     CDC25B      ATMIN      MPZL1 
         5         -7          7          3          4         -7         -4         -4         -7         -4         -6         -5         -6 
   IL13RA1      PSRC1       PGM1   KIAA0196       EXT1     PTPN12       TWF2       TJP1       MEST      ALDOC      ACAA1      KDM5A      RAI14 
         7         -4         -3          6          7         -6         -5         -4          7          5          4         -6          7 
     BIRC2       PAF1       RALB     ARFIP2    ARHGAP1      CPNE3       ABL1      TRAK2      NUP62       PCM1       BLMH        MVP      PLOD3 
        -6          7         -6         -6          4         -4         -4         -7         -7         -7         -4          7          5 
     ARL4C   KIAA0907        CRK       PLK1       CDK4       MTA1     STXBP1      VPS72       FEZ2      SENP6      ACBD3        CSK     CSNK1E 
         5         -3         -3         -7         -6          3         -5          4         -3         -7         -7         -4          6 
     TRIM2       RGS2      ABCF3     TCERG1       USP1        MYC    SLC35B1      DECR1      PAPD7      H2AFV     IKBKAP      BCL7B      HMGCR 
         5         -4         -6         -7         -6         -5         -4          6          6          7         -6         -7          5 
     NRIP1    HTATSF1     ADAM10       EAPP        LYN     APPBP2     POLR2K      ICAM1     PSMB10       SDHB      RASA1     GTF2A2       NPC1 
        -7          7         -5         -6          6          3         -4          6          4         -3         -3         -4         -4 
    GTF2E2       RNMT     RBM15B      OXSR1     DUSP11      CCNB2  HIST2H2BE      PTPN1        TES        EBP       PHKB     PIK3R3        WRB 
        -7         -7          5         -6          7         -7          7          5          4         -4          7          3         -4 
      GPC1      CASP3    DNTTIP2      ZMYM2      OXCT1   MAPKAPK3      INPP1     SACM1L     PRKACA      INTS3     STAMBP        GAA     TARBP1 
         7          4         -3         -6          5          3         -5         -6          6         -6         -7          4          6 
   SLC37A4       PCK2        FAH       POP4      CDC20      CYTH1       NIT1      NUP88       LSM5       MSH6     FAM20B       FHL2       CRYZ 
        -6          6          7         -7         -7          4          7         -6         -3         -7          4         -6         -4 
     UBE2C       RFX5      ARNT2      POLD4     LYPLA1        ECD      PTPRK   TIMELESS      STK10       TCTA       PDHX      PTK2B    TP53BP2 
        -7         -5          7         -4         -5         -5          6          3          7          3         -6          7          4 
   SLC11A2     SPTLC2        TBP       HAT1      TIMP2       PMM2      MTFR1       CDK1    ST3GAL5      MAPK9       TLE1       IL4R      NPRL2 
         5         -6         -7          3          7          6          6         -5          5          6         -6          7          5 
    FBXO11       CDH3       DFFA      EDEM1     HS2ST1   KIAA0355      CNOT4      DMTF1        DCK      BAMBI       NCK2        IDE    PPP2R5E 
        -5          5          7          5          5          4         -7          4         -7          5         -5         -3          4 
     CEBPZ       MTF2       EZH2     DUSP14      SOCS2       APOE      PSMG1       DDB2      CCNA2       EML3        SPR       EPN2     MRPL19 
        -5         -7         -6         -3          7          6         -7         -6         -7          7         -4          6         -3 
   TRAPPC3       STX4      IPO13      MNAT1        AGL      LOXL1    CSNK2A2      RAB4A      IGF1R      FGFR2      HMOX1      NUCB2       BCL2 
        -7          7          7         -6          5          3          7         -5         -4          7         -5          4          6 
      FZD7    GADD45A      BUB1B      BLVRA   SLC25A13      AKAP8      RAB21    RAP1GAP      TCEA2     NFKBIE     MRPL12      CEBPD      WASF3 
        -6          7          7         -5         -5         -6          7          4          7          7         -7          7          4 
      PRKX     SLC5A6     MAP3K4      AURKA       CCNH      TESK1      CDC45      FOXO3     IFNAR1       RTN2      GNA11     ELOVL6     PMAIP1 
         7          3         -7         -7          3          7          7         -4          7          7         -4         -5          7 
    PIK3CA      GSTM2      FOSL1       FZD1       SNCA       MMP1    PIK3C2B        BID       DPH2      BRCA1 ST6GALNAC2      IKBKE     CGRRF1 
         6          5         -3          7          5          6         -4          6         -3         -7          3          6         -6 
       ACD     TFAP2A   KIAA0753       NCK1      PARP2     MAP2K5     C2CD2L     USP6NL        FAS       PPOX      TMEM5       CLPX       ZW10 
         5          7          6         -7         -7          5          7         -6         -3          7         -5         -7         -4 
      MELK       CCNF      RAD9A      ICAM3   TRAPPC6A     CDK5R1       ATF5       LSM6      CENPE        KIT      ITGAE       IL1B       ORC1 
        -4         -7         -5         -5          7          5         -3         -5         -3          7          5          6          7 
      SGCB       CD40       CLTB       PLS1      PCMT1      GNA15       CBR3      CHEK1      SMAD3      PHKA1      FOXO4      PDGFA     CASP10 
         3          7          6          3         -6          7         -3         -4         -6          5         -3         -7          7 
        C5        BTK      RPP38       SNX7       NOS3      SCYL3      ALAS1       BPHL      POLG2     HMGCS1      NOLC1     NFATC4      CCNA1 
         7          6         -7          7          5         -6          6          4         -4         -7         -5          7          5 
     POLE2       TBX2      FOXJ3     RAD51C      EPHA3       FUT1       CRKL        EGF      KIF14       GLRX      CPSF4      LPAR2       DFFB 
        -7          4         -5          4          3          7          5          6         -6         -7          6          4          6 
   SLC35A3       GLI2     CDKN2A       E2F2      CASP7     TGFBR2       RAC2     POLR1C      NFKB2        SYK     TBXA2R    GADD45B       CASK 
        -3          6          3          7         -6         -6          4          3          4          5          6          3         -5 
     PSMD9      PROS1      CASC3        NVL      PPARD      CASP2        LSR       EIF5       CBLB      TBPL1    XPNPEP1       XPO7        BAX 
         4          3         -5          7          7         -5          7         -5          6         -4         -3         -6          6 
    SPTAN1     EIF4G1       VAT1      FDFT1      HSPA8     PDLIM1      OXA1L      CDC42      HSPA4       ADH5       CYCS     LGALS8    ALDH7A1 
        -3          4         -3         -4         -7          4         -5         -6          7         -3          5          7          7 
    DNAJB6     COPS7A      PSMB8     CORO1A      GLOD4        DLD      IFRD2     CDKN1B      PRPF4     MAN2B1        FOS      TUBB6      CXCR4 
         6          6         -3          4         -7         -3         -3         -6         -6          7          7         -3          5 
      CBR1        SFN      NR2F6      NSDHL      IKBKB      KIF2C      AURKB       RPA3     RAB27A      GSTZ1        EED      PRUNE      EPHB2 
         3         -3         -4         -4          7         -6          6         -5          4          3         -6         -3          5 
 HIST1H2BK      PUF60     ATP2C1      PRKCQ     ZNF589     IGFBP3     RPL39L    PLA2G4A      CHEK2       GRB7      DHRS7      ERBB2       CDK7 
         3         -7          3          7          6          6         -3          7         -7          7         -3         -7         -7 
      BMP4      CDK19      VDAC1      WIPF2       HN1L      PDS5A       COG4     FBXO21     TMEM97      VGLL4      UBE3B     SPRED2    GPATCH8 
         6         -4         -4         -4         -4         -5          7          3         -7         -5          7          7         -7 
 MAPK1IP1L        ADO      GAPDH       CHN1      DHX29     TIPARP      KDM3A    PLEKHM1     PIK3R4    CAMSAP2   KIAA1033      ASCC3   SLC25A46 
        -7         -7         -3          4         -4          3         -7          7         -5          6         -7         -5         -6 
     RRP1B    DCUN1D4   MAPKAPK5      C2CD2       WDR7    SUPV3L1     THAP11       RFNG      APBB2     HOXA10       COG7     TICAM1      GDPD5 
        -7          3         -4          3          7          7         -4          6          6         -5          7          3          7 
     PLCB3      SPDEF      FCHO1       NENF       SOX2      HOXA5    TMEM110     NFKBIB     ARID4B       RALA     ARPP19      CCNB1      RBM34 
         5          3          6          5          7         -3          7          6         -3          3         -5         -6         -5 
      DNM1      WDR61     AKAP8L    IGHMBP2   PPP1R13B       CCL2       NGRN       ADI1      RAB31    TMEM50A       YKT6     UBE2J1        EVL 
         4         -6          7          5          7          3          7          3          5         -3         -7          7          4 
     BACE2     PIH1D1      CAB39      IARS2       BAG3       LAP3      STUB1     ENOPH1      SQRDL      MRPS2      NUP85     NUSAP1     MRPS16 
         6          6         -6         -5         -6          6         -3         -7          4         -7         -7         -6         -6 
     NPDC1       UBR7      TMEM2     ZNF395      ADCK3      ISOC1     CCDC92     GOLT1B     SCAND1      NR1H2       TSKU     ZDHHC6      TIMM9 
         6         -3         -5          7         -3          5          3         -4         -6          5         -5         -4         -7 
      GMNN     CRELD2      NUDT9      CDCA4       CERK      KCTD5      CD320      DHDDS    SUV39H1      VPS28      NARFL      CHMP6     KIF20A 
         6          7         -6         -7          7          6          5          7         -7         -6          7          6         -7 
     HOOK2       VAV3    SLC35F2    IGF2BP2     FAM57A     NOTCH1      ANO10    FASTKD5      LAGE3     AMDHD2     PRR15L       FSD1     TIMM22 
         3          6         -7         -4         -5          7          5         -6          3          4          7          7          7 
      RBKS      CHAC1       MSRA      ADAT1     FKBP14      CHIC2       PRR7      SPAG4     MCOLN1     SLC2A6     FBXL12      SNX11       ATG3 
         3          7          5          7          3         -3          6          4          7         -3          6         -7         -7 
      FAIM     GTPBP8       PECR       FRS2     BNIP3L      GRWD1      ABHD6      SIRT3      STAP2      ACOT9     YTHDF1    MICALL1     FAM63A 
         5         -6          6          7         -6         -6          7          5          7         -7         -6         -7          5 
     P4HTM    SLC27A3      MACF1     NPEPL1 
         6          6         -7          5 
  
  print("Check that genes are all in the right order... ")
[1] "Check that genes are all in the right order... "
  head(rownames(overlap) == names(cmpd_ordered2))
[1] TRUE TRUE TRUE TRUE TRUE TRUE
  
  #
  head(rownames(overlap))
[1] "DDR1"   "PAX8"   "SCARB1" "PTPRC"  "JMJD6"  "TLR4"  
  head(names(cmpd_ordered2))
[1] "DDR1"   "PAX8"   "SCARB1" "PTPRC"  "JMJD6"  "TLR4"  
  

Now set up each different tumor type as a vector or whatever to be able to calculate SC for each…

# SHH
head(overlap)
SHH <- overlap$Log2FC_SHH
names(SHH) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
[1] "Check that genes are all in the right order... "
head(names(SHH) == names(cmpd_ordered2))
[1] TRUE TRUE TRUE TRUE TRUE TRUE
SC.SHH <- cor(cmpd_ordered2, SHH, method = "spearman")
  
# WNT
head(overlap)
WNT <- overlap$Log2FC_WNT
names(WNT) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
[1] "Check that genes are all in the right order... "
head(names(WNT) == names(cmpd_ordered2))
[1] TRUE TRUE TRUE TRUE TRUE TRUE
SC.WNT <- cor(cmpd_ordered2, WNT, method = "spearman")
# G3
head(overlap)
G3 <- overlap$Log2FC_G3
names(G3) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
[1] "Check that genes are all in the right order... "
head(names(G3) == names(cmpd_ordered2))
[1] TRUE TRUE TRUE TRUE TRUE TRUE
SC.G3 <- cor(cmpd_ordered2, G3, method = "spearman")
# G4
head(overlap)
G4 <- overlap$Log2FC_G4
names(G4) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
[1] "Check that genes are all in the right order... "
head(names(G4) == names(cmpd_ordered2))
[1] TRUE TRUE TRUE TRUE TRUE TRUE
SC.G4 <- cor(cmpd_ordered2, G4, method = "spearman")

So how do we make a figure showing that g3 is predicted over SHH, others?

First, can we subset to a signature that we can visualize by thresholding on fold change?

G3
         DDR1          PAX8        SCARB1         PTPRC         JMJD6          TLR4         CNPY3       PIP4K2B         SNX13         MBNL2 
-0.0487913995 -0.0456389716  0.0671821998 -0.0601250512  0.0218637272 -0.0027584795  0.0154718710 -0.0025910950  0.0084135208  0.0113432566 
        MYO10        TXNDC9        DNAJA3         ATP5S         CANT1          GNB5         TRAM2         FBXO7         CRTAP         GFOD1 
-0.0108054138  0.0061185887  0.0122281680  0.0577420351  0.0296763550  0.1271499568 -0.0024948390  0.0172462715  0.0529278086 -0.0043345685 
       ATP11B        PSMD10       ARHGEF2         TOR1A         PSIP1         FGFR4         PTGS2        LPGAT1        STAT5B          TERT 
 0.0339939938 -0.0033599835 -0.0116381543  0.0099320197 -0.0485907715  0.0121498913  0.1358661365  0.0914431120  0.0024034206  0.0400260350 
         ETS1         ASAH1          RNH1         TGFB3         MBNL1        CDC25A          RHEB         TRIB3       CSNK1A1          SPEN 
 0.0455765383 -0.0021849718 -0.0283059245  0.0278543655  0.0092557947  0.0974301353 -0.0203703941  0.0620026195  0.0079036509 -0.0172002103 
       HOMER2         ITFG1         TSEN2        HEATR1         PHKG2        FAM69A        COL1A1        SNAP25          RBM6         TCTN1 
 0.0221950810 -0.0340932090  0.0234017567  0.0624601626 -0.0530654267  0.0876332283  0.0639033184  0.0413275837  0.0251457060 -0.0230862630 
        BLCAP        NT5DC2          SMC3         KIF5C         G3BP1        MYCBP2        ZNF131           SHB          PCCB          GALE 
-0.0596925965  0.0265246260 -0.0126004150 -0.0629647250  0.0224906783  0.0220867747 -0.0159616896 -0.0234346664  0.0172679810 -0.0125718987 
         CD44        CTNND1        ARID5B           SRC          ATF1         SYNE2          TPM1         SSBP2        MAP4K4          NOL3 
 0.0391607188 -0.0112518805 -0.0106911660  0.0103025376  0.0061149900 -0.0349941982  0.0629030915 -0.0411937117 -0.0355996470 -0.0341710010 
         RRP8         RRP12         KAT6A          PTK2      ARHGEF12       TIMM17B         DDX42         FKBP4         MKNK1         DYRK3 
 0.0371995690 -0.0119740532  0.0021422910  0.0332210545 -0.0037243458  0.0044308205  0.0151818017  0.0392512125 -0.0622793217  0.0272393535 
         RSU1        TXNRD1         TXLNA         CCND3         NCOA3         CNDP2         DDX10         HERC6        INPP4B          CAST 
 0.0348442020 -0.0054602055  0.0281651330 -0.0376397030  0.0299873562 -0.0328274480  0.0489106915  0.0730577500 -0.0102534287  0.0256840752 
         EDN1          EGFR        TATDN2        PRSS23         IKZF1         SUZ12         KCNK1          MMP2        NFE2L2          SOX4 
-0.1278627510 -0.1007566044  0.0245395600 -0.0357736805 -0.0119893693  0.0172974143 -0.1488072805 -0.0057805607 -0.0062287560 -0.0384272088 
        CHERP      SERPINE1         IGF2R       SMARCA4       TP53BP1        TRIM13          PRCP        CCP110       PPP2R3C        STXBP2 
-0.0237510280  0.1047675547  0.0175329613  0.0220214716  0.0051658690 -0.0078431125  0.0045343412  0.0321315360  0.0085368607 -0.0142944105 
          BAD          RPS5         ABCF1         SPAG7         RNPS1        SMNDC1       ATP6V0B          RPS6         USP22          CLTC 
-0.0242980633  0.0418646700  0.0361638410  0.0208820670  0.0010829485  0.0076570610  0.0343444160  0.0129438745 -0.0684802594  0.0303607217 
        CSRP1         PTPRF        DNAJB1          XBP1           GRN           HK1          CALU          CTSD         MAT2A          GNAS 
-0.0289263220  0.1314562600  0.0676783115  0.0354088515 -0.0427482113 -0.1219285910  0.0200435566 -0.0281243630  0.0237300105  0.0204870821 
         ECH1        IQGAP1        HSPA1A         HSPD1      PAFAH1B1         HYOU1         PSMD2          EPRS         PSMD4        TMED10 
 0.0050745620  0.0386016013  0.0245368413  0.0491196886  0.0360722770 -0.0045511980 -0.0147643630  0.0583034673  0.0402127935  0.0301930393 
        HIF1A         PAICS         PSMF1          MYL9       SMARCC1        TM9SF2           PXN         COPB2          PFKL         ITGB5 
-0.0027407920  0.0710722713  0.0049828038  0.0164958505  0.0356057590  0.0389588440 -0.0198596940  0.0078831495 -0.0280452660 -0.0135798330 
         ACLY          PLP2       BHLHE40       TERF2IP         HTRA1        LRPAP1         CREG1          PCNA          LGMN        ATP1B1 
 0.0598630563  0.1206142090 -0.0181385460 -0.0685826230 -0.0933477130  0.0041991830 -0.0188762570  0.0331951580  0.0314705190  0.0595998550 
        SYPL1        NUDCD3         TOP2A      EBNA1BP2          SCP2         ANXA7       TPD52L2         TRAP1           CAT      MAPKAPK2 
 0.0140339560 -0.0595639817  0.0632546870  0.0374547680  0.0607202640 -0.0056094300 -0.0179389010 -0.0455588500 -0.0061536153 -0.0733902277 
          JUN          SHC1        SQSTM1          USP7        NFKBIA       TOMM70A         ZFP36         KDM5B          MCM3          RAE1 
 0.0617870627  0.0182114755 -0.0302412523 -0.0187025070  0.0663207360  0.1033180165 -0.0978937550  0.0144580724  0.0203954360 -0.0158568543 
        CLIC4           ID2         NISCH          PWP1        RUVBL1        MBTPS1        INSIG1         RRAGA          IER3        UBE2L6 
 0.0379038180  0.0405363615  0.0763931440  0.0180408903  0.0248210410 -0.0599090065  0.0054039438 -0.0624999190  0.0146784020 -0.1124652210 
         SMC4         USP14           PNP         DNMT1         MYBL2          RPA2        MTHFD2          DAXX         ELAC2        NCAPD2 
 0.0711149053  0.0188244610  0.0689846150  0.0393505820  0.1086395350 -0.0030789480  0.0997487690  0.0072002770 -0.0076372625  0.0415195860 
          LBR        SCCPDH          NET1         HDAC2         BNIP3        CDC25B         ATMIN         MPZL1       IL13RA1         PSRC1 
 0.0016582240  0.0178712280  0.0096862890  0.0012021520 -0.0090135090  0.0069597080 -0.0616725580  0.0014480237 -0.0243491725 -0.0628945730 
         PGM1      KIAA0196          EXT1        PTPN12          TWF2          TJP1          MEST         ALDOC         ACAA1         KDM5A 
-0.0898818470  0.0395921920  0.0079204933  0.0055204990 -0.0613615960 -0.0198833890 -0.0477617650 -0.2632686900 -0.0022367505  0.0083126624 
        RAI14         BIRC2          PAF1          RALB        ARFIP2       ARHGAP1         CPNE3          ABL1         TRAK2         NUP62 
-0.0084580160  0.0026388660 -0.0370873620  0.0303013325  0.0073244900 -0.0363666817  0.0448785945 -0.0031702500  0.1188727050 -0.0155467227 
         PCM1          BLMH           MVP         PLOD3         ARL4C      KIAA0907           CRK          PLK1          CDK4          MTA1 
 0.0493880670  0.0378235920 -0.0308943890 -0.0154721620 -0.0511524302  0.0541267885  0.0269962133  0.0431637310  0.0006805000  0.0164722705 
       STXBP1         VPS72          FEZ2         SENP6         ACBD3           CSK        CSNK1E         TRIM2          RGS2         ABCF3 
-0.0786880890 -0.0211930710  0.0684414280 -0.0020569627  0.0075083425 -0.0379082670 -0.0284993990 -0.0549893183  0.0639930700 -0.0004122800 
       TCERG1          USP1           MYC       SLC35B1         DECR1         PAPD7         H2AFV        IKBKAP         BCL7B         HMGCR 
 0.0449700223  0.0054634865  0.4261564470  0.0349244910 -0.0496953110 -0.0039645600 -0.0293456115 -0.0180228085  0.0049291950  0.0649062065 
        NRIP1       HTATSF1        ADAM10          EAPP           LYN        APPBP2        POLR2K         ICAM1        PSMB10          SDHB 
 0.0146296410 -0.0034657545  0.0150399656 -0.0010762830 -0.1521439300 -0.0226747180  0.0864680700 -0.0284914557 -0.1004491850  0.0401067590 
        RASA1        GTF2A2          NPC1        GTF2E2          RNMT        RBM15B         OXSR1        DUSP11         CCNB2     HIST2H2BE 
 0.0102267055  0.0208596643 -0.0169537902  0.0339688180 -0.0055300275  0.0029150010  0.0102668500  0.0056611960 -0.0716007450  0.0370291620 
        PTPN1           TES           EBP          PHKB        PIK3R3           WRB          GPC1         CASP3       DNTTIP2         ZMYM2 
 0.0041042418 -0.0598638523  0.0461429310 -0.0509563675  0.0349836620  0.0003100470 -0.0531062870  0.0067878890  0.0233123100  0.0304811319 
        OXCT1      MAPKAPK3         INPP1        SACM1L        PRKACA         INTS3        STAMBP           GAA        TARBP1       SLC37A4 
-0.0123781090 -0.0420204190 -0.0520295680  0.0479078350 -0.0106772110  0.0009519780  0.0122075807 -0.0861673290 -0.0072398350  0.0613654825 
         PCK2           FAH          POP4         CDC20         CYTH1          NIT1         NUP88          LSM5          MSH6        FAM20B 
 0.1925205080 -0.0226648665  0.0072525950  0.0850953490 -0.0408102610 -0.0066087260  0.0251438885  0.0298526821 -0.0071003897  0.0794342415 
         FHL2          CRYZ         UBE2C          RFX5         ARNT2         POLD4        LYPLA1           ECD         PTPRK      TIMELESS 
-0.0463779680  0.1492747130  0.0355885250  0.0553355320 -0.0790274060 -0.0167739480  0.1457716265  0.0318681920 -0.2782815455 -0.0091321410 
        STK10          TCTA          PDHX         PTK2B       TP53BP2       SLC11A2        SPTLC2           TBP          HAT1         TIMP2 
-0.0072698270  0.0319208060  0.0361207050 -0.1000499355 -0.0088880050  0.0218464846  0.0373247476 -0.0048597700  0.0460268700  0.0037885430 
         PMM2         MTFR1          CDK1       ST3GAL5         MAPK9          TLE1          IL4R         NPRL2        FBXO11          CDH3 
 0.0512669700  0.0929995660  0.0295286423 -0.0096539650 -0.0360034040 -0.2104426214  0.0100097050 -0.0285424320 -0.0103206912 -0.3558887030 
         DFFA         EDEM1        HS2ST1      KIAA0355         CNOT4         DMTF1           DCK         BAMBI          NCK2           IDE 
 0.0365565933  0.0163508060  0.0426744190 -0.0218880410 -0.0002025818  0.0086796370 -0.0087063860 -0.0358097550 -0.0635844930  0.0480001577 
      PPP2R5E         CEBPZ          MTF2          EZH2        DUSP14         SOCS2          APOE         PSMG1          DDB2         CCNA2 
 0.0292587112  0.0250261900  0.0238005616 -0.0244844470  0.0050371790 -0.1199871803 -0.0799151148  0.1374729900 -0.0066459520  0.0602552180 
         EML3           SPR          EPN2        MRPL19       TRAPPC3          STX4         IPO13         MNAT1           AGL         LOXL1 
-0.0218988256  0.0358713790 -0.0423238010  0.0475340163  0.0156739170  0.0045477390 -0.0043635900  0.0360090860  0.0194218190  0.1454031580 
      CSNK2A2         RAB4A         IGF1R         FGFR2         HMOX1         NUCB2          BCL2          FZD7       GADD45A         BUB1B 
 0.0209286365  0.0321262143  0.0381824546  0.0058611016 -0.0360414410  0.0105821040  0.0220775573  0.1659426030  0.0927515300  0.1017785420 
        BLVRA      SLC25A13         AKAP8         RAB21       RAP1GAP         TCEA2        NFKBIE        MRPL12         CEBPD         WASF3 
 0.0004777544 -0.0065798253  0.0166237495  0.0289916775  0.0466771485 -0.1103100913 -0.0450364730  0.0048064920  0.0031264550  0.0349280090 
         PRKX        SLC5A6        MAP3K4         AURKA          CCNH         TESK1         CDC45         FOXO3        IFNAR1          RTN2 
-0.1260799940  0.1094041140  0.0773074755  0.0640982363 -0.0300515610 -0.0274854530  0.0220929060 -0.0403288266 -0.0480499195 -0.0178101380 
        GNA11        ELOVL6        PMAIP1        PIK3CA         GSTM2         FOSL1          FZD1          SNCA          MMP1       PIK3C2B 
-0.0293040742 -0.0339570957 -0.0613600785 -0.0417947877 -0.0201982280 -0.0627816770  0.1762483483 -0.2755466862  0.0708894660 -0.0612959910 
          BID          DPH2         BRCA1    ST6GALNAC2         IKBKE        CGRRF1           ACD        TFAP2A      KIAA0753          NCK1 
-0.0134585653  0.0174793530 -0.0073485635  0.0334383480  0.0131955425  0.0079485660 -0.1070586140 -0.0104502487  0.0226208500  0.0090977902 
        PARP2        MAP2K5        C2CD2L        USP6NL           FAS          PPOX         TMEM5          CLPX          ZW10          MELK 
 0.0181871887 -0.0259556635  0.0468601725  0.0394232927 -0.0642531238  0.0001677213  0.0010082140  0.0182277220  0.0655491440  0.0554313500 
         CCNF         RAD9A         ICAM3      TRAPPC6A        CDK5R1          ATF5          LSM6         CENPE           KIT         ITGAE 
 0.0910164000 -0.0398008800 -0.1171768820 -0.0507576210 -0.0401874820  0.0366278757  0.0291714310  0.0960813850  0.0557225050  0.0394208660 
         IL1B          ORC1          SGCB          CD40          CLTB          PLS1         PCMT1         GNA15          CBR3         CHEK1 
-0.0634881170  0.0192622850 -0.0741192253 -0.0163640265 -0.0400246417  0.0954317550  0.0203483473 -0.0095179040 -0.1874947770  0.0638720947 
        SMAD3         PHKA1         FOXO4         PDGFA        CASP10            C5           BTK         RPP38          SNX7          NOS3 
 0.0265305207  0.0090868115 -0.0132118640 -0.0488589120 -0.0139226063 -0.1664309980 -0.0433042490  0.0326883670  0.0762309600  0.2551925070 
        SCYL3         ALAS1          BPHL         POLG2        HMGCS1         NOLC1        NFATC4         CCNA1         POLE2          TBX2 
 0.0206822360  0.0140141640 -0.0481556010  0.0144717770  0.0343635995  0.0200803193 -0.0344002043 -0.0606241650  0.0612519160 -0.0177039720 
        FOXJ3        RAD51C         EPHA3          FUT1          CRKL           EGF         KIF14          GLRX         CPSF4         LPAR2 
 0.0047537745  0.0375387645 -0.0020513613 -0.0314414070  0.0167465915  0.0370524820  0.1121642050  0.0147019070  0.0028355780 -0.0414470750 
         DFFB       SLC35A3          GLI2        CDKN2A          E2F2         CASP7        TGFBR2          RAC2        POLR1C         NFKB2 
 0.0419555390 -0.0053591393 -0.0429800967 -0.0310670937  0.0557267883 -0.0400631390  0.0535987400 -0.0728361715  0.0671416890 -0.0436350183 
          SYK        TBXA2R       GADD45B          CASK         PSMD9         PROS1         CASC3           NVL         PPARD         CASP2 
 0.3033506405  0.0052436170  0.0002465720  0.0018948756  0.0414859960 -0.0214299510 -0.0466005970  0.0388635120 -0.0186341788  0.0017548894 
          LSR          EIF5          CBLB         TBPL1       XPNPEP1          XPO7           BAX        SPTAN1        EIF4G1          VAT1 
-0.0493698040  0.0184341866  0.0961424887 -0.0009599480  0.0243466713  0.0352471600  0.0163260005 -0.0222047438  0.0365872855 -0.0683949740 
        FDFT1         HSPA8        PDLIM1         OXA1L         CDC42         HSPA4          ADH5          CYCS        LGALS8       ALDH7A1 
 0.0597294020  0.0275706198  0.1391876200  0.0651224640  0.0261411392  0.0631597640  0.0039192185 -0.0015603430  0.0440354662 -0.0077360377 
       DNAJB6        COPS7A         PSMB8        CORO1A         GLOD4           DLD         IFRD2        CDKN1B         PRPF4        MAN2B1 
 0.0400052450 -0.0120776940  0.2495461400 -0.1049919910 -0.0273326700  0.0502410805  0.0357135240  0.0048221350  0.0151667355  0.0168853090 
          FOS         TUBB6         CXCR4          CBR1           SFN         NR2F6         NSDHL         IKBKB         KIF2C         AURKB 
-0.0458717540 -0.0156289180  0.0365443747  0.0138730190 -0.0218581960  0.0678360577  0.0299633965  0.0284543967  0.0830795220  0.0859259190 
         RPA3        RAB27A         GSTZ1           EED         PRUNE         EPHB2     HIST1H2BK         PUF60        ATP2C1         PRKCQ 
 0.0530351240 -0.0115720332  0.0335273790  0.0539727110  0.0350543710 -0.0394641054  0.0520147260  0.0134849040  0.0735162547  0.0404867330 
       ZNF589        IGFBP3        RPL39L       PLA2G4A         CHEK2          GRB7         DHRS7         ERBB2          CDK7          BMP4 
 0.0191211817  0.0622789575 -0.0622300040  0.0198653090  0.0262729950 -0.0181197410  0.0233031007 -0.0662874033  0.0535293980 -0.0292045400 
        CDK19         VDAC1         WIPF2          HN1L         PDS5A          COG4        FBXO21        TMEM97         VGLL4         UBE3B 
-0.0344775352  0.0083247847 -0.0226782168  0.0004037753  0.0363618365 -0.0958521790 -0.0329883257  0.0322847110 -0.1245172805  0.0157846815 
       SPRED2       GPATCH8     MAPK1IP1L           ADO         GAPDH          CHN1         DHX29        TIPARP         KDM3A       PLEKHM1 
 0.0151260123 -0.0072624850  0.0106710925 -0.0091692450  0.0140014782 -0.1051355390  0.0242384140  0.0502487700  0.0909427235 -0.0115925455 
       PIK3R4       CAMSAP2      KIAA1033         ASCC3      SLC25A46         RRP1B       DCUN1D4      MAPKAPK5         C2CD2          WDR7 
 0.0066291107  0.0156960267  0.0282974337  0.0646515990  0.0008534460  0.0414089075 -0.0232097217  0.0383117845  0.0402856280 -0.0208450395 
      SUPV3L1        THAP11          RFNG         APBB2        HOXA10          COG7        TICAM1         GDPD5         PLCB3         SPDEF 
-0.0134663710 -0.0305872650 -0.0504759670  0.0288108216  0.0128787805 -0.0476206770  0.1201310820  0.0793159285  0.0333728450  0.0423500932 
        FCHO1          NENF          SOX2         HOXA5       TMEM110        NFKBIB        ARID4B          RALA        ARPP19         CCNB1 
-0.0118323900  0.0141299525 -0.0611985997  0.0788659540  0.0313531060 -0.0021516990  0.0259249195  0.0206823150  0.0093898023  0.0680331705 
        RBM34          DNM1         WDR61        AKAP8L       IGHMBP2      PPP1R13B          CCL2          NGRN          ADI1         RAB31 
-0.0290578820 -0.1018115985  0.0028901950  0.0370965048  0.0132725483  0.0162129180  0.1424147770  0.0036667283  0.0074927940 -0.0780890207 
      TMEM50A          YKT6        UBE2J1           EVL         BACE2        PIH1D1         CAB39         IARS2          BAG3          LAP3 
 0.0210497625  0.0159397940  0.0731200617  0.0074057920 -0.0245869113 -0.0037112750  0.0043392200  0.0586633540 -0.0359330670  0.0353684010 
        STUB1        ENOPH1         SQRDL         MRPS2         NUP85        NUSAP1        MRPS16         NPDC1          UBR7         TMEM2 
-0.0398094837  0.0312823140 -0.0533107540  0.0075857010  0.0125252420  0.0617493280  0.0217226125 -0.0484566490  0.0221665760 -0.0259300750 
       ZNF395         ADCK3         ISOC1        CCDC92        GOLT1B        SCAND1         NR1H2          TSKU        ZDHHC6         TIMM9 
 0.0506821433  0.0122316590  0.1764540910 -0.0495760880  0.0397577700 -0.0215070780 -0.0889810660  0.0496492150  0.0052835320  0.0600677870 
         GMNN        CRELD2         NUDT9         CDCA4          CERK         KCTD5         CD320         DHDDS       SUV39H1         VPS28 
 0.0073228080  0.0206527410  0.0265541420  0.0547367810 -0.0696747570 -0.0171017393  0.0753358300 -0.0545451985 -0.0061926660 -0.0089665520 
        NARFL         CHMP6        KIF20A         HOOK2          VAV3       SLC35F2       IGF2BP2        FAM57A        NOTCH1         ANO10 
-0.0755056980 -0.0538229850  0.0737769920  0.0225532420  0.0052280440  0.0006165820  0.0289402380 -0.0328129570  0.0534230790 -0.0043653940 
      FASTKD5         LAGE3        AMDHD2        PRR15L          FSD1        TIMM22          RBKS         CHAC1          MSRA         ADAT1 
 0.0275351460 -0.0140379190 -0.1922636650  0.0347196440 -0.1779230860 -0.0020847937  0.0737755380  0.0236545150 -0.1316496870 -0.0718148460 
       FKBP14         CHIC2          PRR7         SPAG4        MCOLN1        SLC2A6        FBXL12         SNX11          ATG3          FAIM 
 0.0170483917 -0.0017746890  0.0211565820  0.0658832550 -0.0060871320  0.1017468040  0.0026517195  0.0182990100  0.0222526545  0.0785146920 
       GTPBP8          PECR          FRS2        BNIP3L         GRWD1         ABHD6         SIRT3         STAP2         ACOT9        YTHDF1 
-0.0086561470 -0.0065644375  0.0047739027  0.0021209925  0.0377533780 -0.0540747987 -0.0033130537  0.0137236800  0.0332240610 -0.0083579240 
      MICALL1        FAM63A         P4HTM       SLC27A3         MACF1        NPEPL1 
 0.0310617985 -0.0696536875 -0.0077015290 -0.1012534970 -0.0296154260  0.0172414015 
df <- as.data.frame(G3)
df
                      G3
DDR1       -0.0487913995
PAX8       -0.0456389716
SCARB1      0.0671821998
PTPRC      -0.0601250512
JMJD6       0.0218637272
TLR4       -0.0027584795
CNPY3       0.0154718710
PIP4K2B    -0.0025910950
SNX13       0.0084135208
MBNL2       0.0113432566
MYO10      -0.0108054138
TXNDC9      0.0061185887
DNAJA3      0.0122281680
ATP5S       0.0577420351
CANT1       0.0296763550
GNB5        0.1271499568
TRAM2      -0.0024948390
FBXO7       0.0172462715
CRTAP       0.0529278086
GFOD1      -0.0043345685
ATP11B      0.0339939938
PSMD10     -0.0033599835
ARHGEF2    -0.0116381543
TOR1A       0.0099320197
PSIP1      -0.0485907715
FGFR4       0.0121498913
PTGS2       0.1358661365
LPGAT1      0.0914431120
STAT5B      0.0024034206
TERT        0.0400260350
ETS1        0.0455765383
ASAH1      -0.0021849718
RNH1       -0.0283059245
TGFB3       0.0278543655
MBNL1       0.0092557947
CDC25A      0.0974301353
RHEB       -0.0203703941
TRIB3       0.0620026195
CSNK1A1     0.0079036509
SPEN       -0.0172002103
HOMER2      0.0221950810
ITFG1      -0.0340932090
TSEN2       0.0234017567
HEATR1      0.0624601626
PHKG2      -0.0530654267
FAM69A      0.0876332283
COL1A1      0.0639033184
SNAP25      0.0413275837
RBM6        0.0251457060
TCTN1      -0.0230862630
BLCAP      -0.0596925965
NT5DC2      0.0265246260
SMC3       -0.0126004150
KIF5C      -0.0629647250
G3BP1       0.0224906783
MYCBP2      0.0220867747
ZNF131     -0.0159616896
SHB        -0.0234346664
PCCB        0.0172679810
GALE       -0.0125718987
CD44        0.0391607188
CTNND1     -0.0112518805
ARID5B     -0.0106911660
SRC         0.0103025376
ATF1        0.0061149900
SYNE2      -0.0349941982
TPM1        0.0629030915
SSBP2      -0.0411937117
MAP4K4     -0.0355996470
NOL3       -0.0341710010
RRP8        0.0371995690
RRP12      -0.0119740532
KAT6A       0.0021422910
PTK2        0.0332210545
ARHGEF12   -0.0037243458
TIMM17B     0.0044308205
DDX42       0.0151818017
FKBP4       0.0392512125
MKNK1      -0.0622793217
DYRK3       0.0272393535
RSU1        0.0348442020
TXNRD1     -0.0054602055
TXLNA       0.0281651330
CCND3      -0.0376397030
NCOA3       0.0299873562
CNDP2      -0.0328274480
DDX10       0.0489106915
HERC6       0.0730577500
INPP4B     -0.0102534287
CAST        0.0256840752
EDN1       -0.1278627510
EGFR       -0.1007566044
TATDN2      0.0245395600
PRSS23     -0.0357736805
IKZF1      -0.0119893693
SUZ12       0.0172974143
KCNK1      -0.1488072805
MMP2       -0.0057805607
NFE2L2     -0.0062287560
SOX4       -0.0384272088
CHERP      -0.0237510280
SERPINE1    0.1047675547
IGF2R       0.0175329613
SMARCA4     0.0220214716
TP53BP1     0.0051658690
TRIM13     -0.0078431125
PRCP        0.0045343412
CCP110      0.0321315360
PPP2R3C     0.0085368607
STXBP2     -0.0142944105
BAD        -0.0242980633
RPS5        0.0418646700
ABCF1       0.0361638410
SPAG7       0.0208820670
RNPS1       0.0010829485
SMNDC1      0.0076570610
ATP6V0B     0.0343444160
RPS6        0.0129438745
USP22      -0.0684802594
CLTC        0.0303607217
CSRP1      -0.0289263220
PTPRF       0.1314562600
DNAJB1      0.0676783115
XBP1        0.0354088515
GRN        -0.0427482113
HK1        -0.1219285910
CALU        0.0200435566
CTSD       -0.0281243630
MAT2A       0.0237300105
GNAS        0.0204870821
ECH1        0.0050745620
IQGAP1      0.0386016013
HSPA1A      0.0245368413
HSPD1       0.0491196886
PAFAH1B1    0.0360722770
HYOU1      -0.0045511980
PSMD2      -0.0147643630
EPRS        0.0583034673
PSMD4       0.0402127935
TMED10      0.0301930393
HIF1A      -0.0027407920
PAICS       0.0710722713
PSMF1       0.0049828038
MYL9        0.0164958505
SMARCC1     0.0356057590
TM9SF2      0.0389588440
PXN        -0.0198596940
COPB2       0.0078831495
PFKL       -0.0280452660
ITGB5      -0.0135798330
ACLY        0.0598630563
PLP2        0.1206142090
BHLHE40    -0.0181385460
TERF2IP    -0.0685826230
HTRA1      -0.0933477130
LRPAP1      0.0041991830
CREG1      -0.0188762570
PCNA        0.0331951580
LGMN        0.0314705190
ATP1B1      0.0595998550
SYPL1       0.0140339560
NUDCD3     -0.0595639817
TOP2A       0.0632546870
EBNA1BP2    0.0374547680
SCP2        0.0607202640
ANXA7      -0.0056094300
TPD52L2    -0.0179389010
TRAP1      -0.0455588500
CAT        -0.0061536153
MAPKAPK2   -0.0733902277
JUN         0.0617870627
SHC1        0.0182114755
SQSTM1     -0.0302412523
USP7       -0.0187025070
NFKBIA      0.0663207360
TOMM70A     0.1033180165
ZFP36      -0.0978937550
KDM5B       0.0144580724
MCM3        0.0203954360
RAE1       -0.0158568543
CLIC4       0.0379038180
ID2         0.0405363615
NISCH       0.0763931440
PWP1        0.0180408903
RUVBL1      0.0248210410
MBTPS1     -0.0599090065
INSIG1      0.0054039438
RRAGA      -0.0624999190
IER3        0.0146784020
UBE2L6     -0.1124652210
SMC4        0.0711149053
USP14       0.0188244610
PNP         0.0689846150
DNMT1       0.0393505820
MYBL2       0.1086395350
RPA2       -0.0030789480
MTHFD2      0.0997487690
DAXX        0.0072002770
ELAC2      -0.0076372625
NCAPD2      0.0415195860
LBR         0.0016582240
SCCPDH      0.0178712280
NET1        0.0096862890
HDAC2       0.0012021520
BNIP3      -0.0090135090
CDC25B      0.0069597080
ATMIN      -0.0616725580
MPZL1       0.0014480237
IL13RA1    -0.0243491725
PSRC1      -0.0628945730
PGM1       -0.0898818470
KIAA0196    0.0395921920
EXT1        0.0079204933
PTPN12      0.0055204990
TWF2       -0.0613615960
TJP1       -0.0198833890
MEST       -0.0477617650
ALDOC      -0.2632686900
ACAA1      -0.0022367505
KDM5A       0.0083126624
RAI14      -0.0084580160
BIRC2       0.0026388660
PAF1       -0.0370873620
RALB        0.0303013325
ARFIP2      0.0073244900
ARHGAP1    -0.0363666817
CPNE3       0.0448785945
ABL1       -0.0031702500
TRAK2       0.1188727050
NUP62      -0.0155467227
PCM1        0.0493880670
BLMH        0.0378235920
MVP        -0.0308943890
PLOD3      -0.0154721620
ARL4C      -0.0511524302
KIAA0907    0.0541267885
CRK         0.0269962133
PLK1        0.0431637310
CDK4        0.0006805000
MTA1        0.0164722705
STXBP1     -0.0786880890
VPS72      -0.0211930710
FEZ2        0.0684414280
SENP6      -0.0020569627
ACBD3       0.0075083425
CSK        -0.0379082670
CSNK1E     -0.0284993990
TRIM2      -0.0549893183
RGS2        0.0639930700
ABCF3      -0.0004122800
TCERG1      0.0449700223
USP1        0.0054634865
MYC         0.4261564470
SLC35B1     0.0349244910
DECR1      -0.0496953110
PAPD7      -0.0039645600
H2AFV      -0.0293456115
IKBKAP     -0.0180228085
BCL7B       0.0049291950
HMGCR       0.0649062065
NRIP1       0.0146296410
HTATSF1    -0.0034657545
ADAM10      0.0150399656
EAPP       -0.0010762830
LYN        -0.1521439300
APPBP2     -0.0226747180
POLR2K      0.0864680700
ICAM1      -0.0284914557
PSMB10     -0.1004491850
SDHB        0.0401067590
RASA1       0.0102267055
GTF2A2      0.0208596643
NPC1       -0.0169537902
GTF2E2      0.0339688180
RNMT       -0.0055300275
RBM15B      0.0029150010
OXSR1       0.0102668500
DUSP11      0.0056611960
CCNB2      -0.0716007450
HIST2H2BE   0.0370291620
PTPN1       0.0041042418
TES        -0.0598638523
EBP         0.0461429310
PHKB       -0.0509563675
PIK3R3      0.0349836620
WRB         0.0003100470
GPC1       -0.0531062870
CASP3       0.0067878890
DNTTIP2     0.0233123100
ZMYM2       0.0304811319
OXCT1      -0.0123781090
MAPKAPK3   -0.0420204190
INPP1      -0.0520295680
SACM1L      0.0479078350
PRKACA     -0.0106772110
INTS3       0.0009519780
STAMBP      0.0122075807
GAA        -0.0861673290
TARBP1     -0.0072398350
SLC37A4     0.0613654825
PCK2        0.1925205080
FAH        -0.0226648665
POP4        0.0072525950
CDC20       0.0850953490
CYTH1      -0.0408102610
NIT1       -0.0066087260
NUP88       0.0251438885
LSM5        0.0298526821
MSH6       -0.0071003897
FAM20B      0.0794342415
FHL2       -0.0463779680
CRYZ        0.1492747130
UBE2C       0.0355885250
RFX5        0.0553355320
ARNT2      -0.0790274060
POLD4      -0.0167739480
LYPLA1      0.1457716265
ECD         0.0318681920
PTPRK      -0.2782815455
TIMELESS   -0.0091321410
STK10      -0.0072698270
TCTA        0.0319208060
PDHX        0.0361207050
PTK2B      -0.1000499355
TP53BP2    -0.0088880050
SLC11A2     0.0218464846
SPTLC2      0.0373247476
TBP        -0.0048597700
HAT1        0.0460268700
TIMP2       0.0037885430
PMM2        0.0512669700
MTFR1       0.0929995660
CDK1        0.0295286423
ST3GAL5    -0.0096539650
MAPK9      -0.0360034040
TLE1       -0.2104426214
IL4R        0.0100097050
NPRL2      -0.0285424320
FBXO11     -0.0103206912
CDH3       -0.3558887030
DFFA        0.0365565933
EDEM1       0.0163508060
HS2ST1      0.0426744190
KIAA0355   -0.0218880410
CNOT4      -0.0002025818
DMTF1       0.0086796370
DCK        -0.0087063860
BAMBI      -0.0358097550
NCK2       -0.0635844930
IDE         0.0480001577
PPP2R5E     0.0292587112
CEBPZ       0.0250261900
MTF2        0.0238005616
EZH2       -0.0244844470
DUSP14      0.0050371790
SOCS2      -0.1199871803
APOE       -0.0799151148
PSMG1       0.1374729900
DDB2       -0.0066459520
CCNA2       0.0602552180
EML3       -0.0218988256
SPR         0.0358713790
EPN2       -0.0423238010
MRPL19      0.0475340163
TRAPPC3     0.0156739170
STX4        0.0045477390
IPO13      -0.0043635900
MNAT1       0.0360090860
AGL         0.0194218190
LOXL1       0.1454031580
CSNK2A2     0.0209286365
RAB4A       0.0321262143
IGF1R       0.0381824546
FGFR2       0.0058611016
HMOX1      -0.0360414410
NUCB2       0.0105821040
BCL2        0.0220775573
FZD7        0.1659426030
GADD45A     0.0927515300
BUB1B       0.1017785420
BLVRA       0.0004777544
SLC25A13   -0.0065798253
AKAP8       0.0166237495
RAB21       0.0289916775
RAP1GAP     0.0466771485
TCEA2      -0.1103100913
NFKBIE     -0.0450364730
MRPL12      0.0048064920
CEBPD       0.0031264550
WASF3       0.0349280090
PRKX       -0.1260799940
SLC5A6      0.1094041140
MAP3K4      0.0773074755
AURKA       0.0640982363
CCNH       -0.0300515610
TESK1      -0.0274854530
CDC45       0.0220929060
FOXO3      -0.0403288266
IFNAR1     -0.0480499195
RTN2       -0.0178101380
GNA11      -0.0293040742
ELOVL6     -0.0339570957
PMAIP1     -0.0613600785
PIK3CA     -0.0417947877
GSTM2      -0.0201982280
FOSL1      -0.0627816770
FZD1        0.1762483483
SNCA       -0.2755466862
MMP1        0.0708894660
PIK3C2B    -0.0612959910
BID        -0.0134585653
DPH2        0.0174793530
BRCA1      -0.0073485635
ST6GALNAC2  0.0334383480
IKBKE       0.0131955425
CGRRF1      0.0079485660
ACD        -0.1070586140
TFAP2A     -0.0104502487
KIAA0753    0.0226208500
NCK1        0.0090977902
PARP2       0.0181871887
MAP2K5     -0.0259556635
C2CD2L      0.0468601725
USP6NL      0.0394232927
FAS        -0.0642531238
PPOX        0.0001677213
TMEM5       0.0010082140
CLPX        0.0182277220
ZW10        0.0655491440
MELK        0.0554313500
CCNF        0.0910164000
RAD9A      -0.0398008800
ICAM3      -0.1171768820
TRAPPC6A   -0.0507576210
CDK5R1     -0.0401874820
ATF5        0.0366278757
LSM6        0.0291714310
CENPE       0.0960813850
KIT         0.0557225050
ITGAE       0.0394208660
IL1B       -0.0634881170
ORC1        0.0192622850
SGCB       -0.0741192253
CD40       -0.0163640265
CLTB       -0.0400246417
PLS1        0.0954317550
PCMT1       0.0203483473
GNA15      -0.0095179040
CBR3       -0.1874947770
CHEK1       0.0638720947
SMAD3       0.0265305207
PHKA1       0.0090868115
FOXO4      -0.0132118640
PDGFA      -0.0488589120
CASP10     -0.0139226063
C5         -0.1664309980
BTK        -0.0433042490
RPP38       0.0326883670
SNX7        0.0762309600
NOS3        0.2551925070
SCYL3       0.0206822360
ALAS1       0.0140141640
BPHL       -0.0481556010
POLG2       0.0144717770
HMGCS1      0.0343635995
NOLC1       0.0200803193
NFATC4     -0.0344002043
CCNA1      -0.0606241650
POLE2       0.0612519160
TBX2       -0.0177039720
FOXJ3       0.0047537745
RAD51C      0.0375387645
EPHA3      -0.0020513613
FUT1       -0.0314414070
CRKL        0.0167465915
EGF         0.0370524820
KIF14       0.1121642050
GLRX        0.0147019070
CPSF4       0.0028355780
LPAR2      -0.0414470750
DFFB        0.0419555390
SLC35A3    -0.0053591393
GLI2       -0.0429800967
CDKN2A     -0.0310670937
E2F2        0.0557267883
CASP7      -0.0400631390
TGFBR2      0.0535987400
RAC2       -0.0728361715
POLR1C      0.0671416890
NFKB2      -0.0436350183
SYK         0.3033506405
TBXA2R      0.0052436170
GADD45B     0.0002465720
CASK        0.0018948756
PSMD9       0.0414859960
PROS1      -0.0214299510
CASC3      -0.0466005970
NVL         0.0388635120
PPARD      -0.0186341788
CASP2       0.0017548894
LSR        -0.0493698040
EIF5        0.0184341866
CBLB        0.0961424887
TBPL1      -0.0009599480
XPNPEP1     0.0243466713
XPO7        0.0352471600
BAX         0.0163260005
SPTAN1     -0.0222047438
EIF4G1      0.0365872855
VAT1       -0.0683949740
FDFT1       0.0597294020
HSPA8       0.0275706198
PDLIM1      0.1391876200
OXA1L       0.0651224640
CDC42       0.0261411392
HSPA4       0.0631597640
ADH5        0.0039192185
CYCS       -0.0015603430
LGALS8      0.0440354662
ALDH7A1    -0.0077360377
DNAJB6      0.0400052450
COPS7A     -0.0120776940
PSMB8       0.2495461400
CORO1A     -0.1049919910
GLOD4      -0.0273326700
DLD         0.0502410805
IFRD2       0.0357135240
CDKN1B      0.0048221350
PRPF4       0.0151667355
MAN2B1      0.0168853090
FOS        -0.0458717540
TUBB6      -0.0156289180
CXCR4       0.0365443747
CBR1        0.0138730190
SFN        -0.0218581960
NR2F6       0.0678360577
NSDHL       0.0299633965
IKBKB       0.0284543967
KIF2C       0.0830795220
AURKB       0.0859259190
RPA3        0.0530351240
RAB27A     -0.0115720332
GSTZ1       0.0335273790
EED         0.0539727110
PRUNE       0.0350543710
EPHB2      -0.0394641054
HIST1H2BK   0.0520147260
PUF60       0.0134849040
ATP2C1      0.0735162547
PRKCQ       0.0404867330
ZNF589      0.0191211817
IGFBP3      0.0622789575
RPL39L     -0.0622300040
PLA2G4A     0.0198653090
CHEK2       0.0262729950
GRB7       -0.0181197410
DHRS7       0.0233031007
ERBB2      -0.0662874033
CDK7        0.0535293980
BMP4       -0.0292045400
CDK19      -0.0344775352
VDAC1       0.0083247847
WIPF2      -0.0226782168
HN1L        0.0004037753
PDS5A       0.0363618365
COG4       -0.0958521790
FBXO21     -0.0329883257
TMEM97      0.0322847110
VGLL4      -0.1245172805
UBE3B       0.0157846815
SPRED2      0.0151260123
GPATCH8    -0.0072624850
MAPK1IP1L   0.0106710925
ADO        -0.0091692450
GAPDH       0.0140014782
CHN1       -0.1051355390
DHX29       0.0242384140
TIPARP      0.0502487700
KDM3A       0.0909427235
PLEKHM1    -0.0115925455
PIK3R4      0.0066291107
CAMSAP2     0.0156960267
KIAA1033    0.0282974337
ASCC3       0.0646515990
SLC25A46    0.0008534460
RRP1B       0.0414089075
DCUN1D4    -0.0232097217
MAPKAPK5    0.0383117845
C2CD2       0.0402856280
WDR7       -0.0208450395
SUPV3L1    -0.0134663710
THAP11     -0.0305872650
RFNG       -0.0504759670
APBB2       0.0288108216
HOXA10      0.0128787805
COG7       -0.0476206770
TICAM1      0.1201310820
GDPD5       0.0793159285
PLCB3       0.0333728450
SPDEF       0.0423500932
FCHO1      -0.0118323900
NENF        0.0141299525
SOX2       -0.0611985997
HOXA5       0.0788659540
TMEM110     0.0313531060
NFKBIB     -0.0021516990
ARID4B      0.0259249195
RALA        0.0206823150
ARPP19      0.0093898023
CCNB1       0.0680331705
RBM34      -0.0290578820
DNM1       -0.1018115985
WDR61       0.0028901950
AKAP8L      0.0370965048
IGHMBP2     0.0132725483
PPP1R13B    0.0162129180
CCL2        0.1424147770
NGRN        0.0036667283
ADI1        0.0074927940
RAB31      -0.0780890207
TMEM50A     0.0210497625
YKT6        0.0159397940
UBE2J1      0.0731200617
EVL         0.0074057920
BACE2      -0.0245869113
PIH1D1     -0.0037112750
CAB39       0.0043392200
IARS2       0.0586633540
BAG3       -0.0359330670
LAP3        0.0353684010
STUB1      -0.0398094837
ENOPH1      0.0312823140
SQRDL      -0.0533107540
MRPS2       0.0075857010
NUP85       0.0125252420
NUSAP1      0.0617493280
MRPS16      0.0217226125
NPDC1      -0.0484566490
UBR7        0.0221665760
TMEM2      -0.0259300750
ZNF395      0.0506821433
ADCK3       0.0122316590
ISOC1       0.1764540910
CCDC92     -0.0495760880
GOLT1B      0.0397577700
SCAND1     -0.0215070780
NR1H2      -0.0889810660
TSKU        0.0496492150
ZDHHC6      0.0052835320
TIMM9       0.0600677870
GMNN        0.0073228080
CRELD2      0.0206527410
NUDT9       0.0265541420
CDCA4       0.0547367810
CERK       -0.0696747570
KCTD5      -0.0171017393
CD320       0.0753358300
DHDDS      -0.0545451985
SUV39H1    -0.0061926660
VPS28      -0.0089665520
NARFL      -0.0755056980
CHMP6      -0.0538229850
KIF20A      0.0737769920
HOOK2       0.0225532420
VAV3        0.0052280440
SLC35F2     0.0006165820
IGF2BP2     0.0289402380
FAM57A     -0.0328129570
NOTCH1      0.0534230790
ANO10      -0.0043653940
FASTKD5     0.0275351460
LAGE3      -0.0140379190
AMDHD2     -0.1922636650
PRR15L      0.0347196440
FSD1       -0.1779230860
TIMM22     -0.0020847937
RBKS        0.0737755380
CHAC1       0.0236545150
MSRA       -0.1316496870
ADAT1      -0.0718148460
FKBP14      0.0170483917
CHIC2      -0.0017746890
PRR7        0.0211565820
SPAG4       0.0658832550
MCOLN1     -0.0060871320
SLC2A6      0.1017468040
FBXL12      0.0026517195
SNX11       0.0182990100
ATG3        0.0222526545
FAIM        0.0785146920
GTPBP8     -0.0086561470
PECR       -0.0065644375
FRS2        0.0047739027
BNIP3L      0.0021209925
GRWD1       0.0377533780
ABHD6      -0.0540747987
SIRT3      -0.0033130537
STAP2       0.0137236800
ACOT9       0.0332240610
YTHDF1     -0.0083579240
MICALL1     0.0310617985
FAM63A     -0.0696536875
P4HTM      -0.0077015290
SLC27A3    -0.1012534970
MACF1      -0.0296154260
NPEPL1      0.0172414015
th <- subset(df, df$G3 > 0.1 | df$G3 < -0.1)
th
                 G3
GNB5      0.1271500
PTGS2     0.1358661
EDN1     -0.1278628
EGFR     -0.1007566
KCNK1    -0.1488073
SERPINE1  0.1047676
PTPRF     0.1314563
HK1      -0.1219286
PLP2      0.1206142
TOMM70A   0.1033180
UBE2L6   -0.1124652
MYBL2     0.1086395
ALDOC    -0.2632687
TRAK2     0.1188727
MYC       0.4261564
LYN      -0.1521439
PSMB10   -0.1004492
PCK2      0.1925205
CRYZ      0.1492747
LYPLA1    0.1457716
PTPRK    -0.2782815
PTK2B    -0.1000499
TLE1     -0.2104426
CDH3     -0.3558887
SOCS2    -0.1199872
PSMG1     0.1374730
LOXL1     0.1454032
FZD7      0.1659426
BUB1B     0.1017785
TCEA2    -0.1103101
PRKX     -0.1260800
SLC5A6    0.1094041
FZD1      0.1762483
SNCA     -0.2755467
ACD      -0.1070586
ICAM3    -0.1171769
CBR3     -0.1874948
C5       -0.1664310
NOS3      0.2551925
KIF14     0.1121642
SYK       0.3033506
PDLIM1    0.1391876
PSMB8     0.2495461
CORO1A   -0.1049920
VGLL4    -0.1245173
CHN1     -0.1051355
TICAM1    0.1201311
DNM1     -0.1018116
CCL2      0.1424148
ISOC1     0.1764541
AMDHD2   -0.1922637
FSD1     -0.1779231
MSRA     -0.1316497
SLC2A6    0.1017468
SLC27A3  -0.1012535
L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)
head(L1000_signature_data)
        AARS ABCB6 ABCC5 ABCF1 ABCF3 ABHD4 ABHD6 ABL1 ACAA1 ACAT2 ACBD3 ACD ACLY ACOT9 ADAM10 ADAT1 ADCK3 ADH5 ADI1 ADO ADRB2 AGL AKAP8 AKAP8L AKR7A2
10-DEBC    0     0     0     0     0     0     0    0     0     3     0   0    0     0      0     0     0    0    0   0     0   0    -3      0      0
        AKT1 ALAS1 ALDH7A1 ALDOA ALDOC AMDHD2 ANKRD10 ANO10 ANXA7 APBB2 APOE APP APPBP2 ARFIP2 ARHGAP1 ARHGEF12 ARHGEF2 ARID4B ARID5B ARL4C ARNT2
10-DEBC   -3     3       0     0     0      0       0     0     0     0    0   0      0      0       0        0       0      0      3     3     0
        ARPP19 ASAH1 ASCC3 ATF1 ATF5 ATF6 ATG3 ATMIN ATP11B ATP1B1 ATP2C1 ATP5S ATP6V0B ATP6V1D AURKA AURKB AXIN1 BACE2 BAD BAG3 BAMBI BAX BCL2 BCL7B
10-DEBC      0     0     0    0    0    0    0     0      0      0     -3     0       0       0     0     0     0     0   0    0     0   0   -3     0
        BDH1 BECN1 BHLHE40 BID BIRC2 BIRC5 BLCAP BLMH BLVRA BMP4 BNIP3 BNIP3L BPHL BRCA1 BTK BUB1B BZW2 C2CD2 C2CD2L C5 CAB39 CALM3 CALU CAMSAP2
10-DEBC    0     0       0   0     0     0     0    0     0    0     0      0    0     0   0     0    0     0      0  0     0     0    0       0
        CANT1 CAPN1 CASC3 CASK CASP10 CASP2 CASP3 CASP7 CAST CAT CBLB CBR1 CBR3 CCDC85B CCDC86 CCDC92 CCL2 CCNA1 CCNA2 CCNB1 CCNB2 CCND1 CCND3 CCNE2
10-DEBC     0     0    -3   -3      0     0     0     0    0   0    0    0    0       0     -5      0    0     0     0     0     0     0     0     0
        CCNF CCNH CCP110 CD320 CD40 CD44 CD58 CDC20 CDC25A CDC25B CDC42 CDC45 CDCA4 CDH3 CDK1 CDK19 CDK2 CDK4 CDK5R1 CDK6 CDK7 CDKN1A CDKN1B CDKN2A
10-DEBC    0    0      0     0    0    0    0     0      0      0     0     0     0    0    3     0    4    0      0    0    0      0      0      0
        CEBPA CEBPD CEBPZ CENPE CEP57 CERK CETN3 CFLAR CGRRF1 CHAC1 CHEK1 CHEK2 CHERP CHIC2 CHMP4A CHMP6 CHN1 CIAPIN1 CIRBP CISD1 CLIC4 CLPX CLSTN1
10-DEBC     0     0     0     0     0    0     0     0      0     0     0     0    -4     0      0     0    0       0     0     0     0    0      0
        CLTB CLTC CNDP2 CNOT4 CNPY3 COASY COG2 COG4 COG7 COL1A1 COL4A1 COPB2 COPS7A CORO1A CPNE3 CPSF4 CREB1 CREG1 CRELD2 CRK CRKL CRTAP CRYZ CSK
10-DEBC    0    0     0     0     0     0    0    0    0      0      0     0      0      0     0     0     0     0      3   0    0     0    0   0
        CSNK1A1 CSNK1E CSNK2A2 CSRP1 CTNNAL1 CTNND1 CTSD CTTN CXCL2 CXCR4 CYB561 CYCS CYTH1 DAG1 DAXX DCK DCTD DCUN1D4 DDB2 DDIT4 DDR1 DDX10 DDX42
10-DEBC       0      0       0     0       0      0    0    0     0     0      0    4     0    0    0   0    0       0    0     0    0     0     0
        DECR1 DENND2D DERA DFFA DFFB DHDDS DHRS7 DHX29 DLD DMTF1 DNAJA3 DNAJB1 DNAJB2 DNAJB6 DNAJC15 DNM1 DNM1L DNMT1 DNMT3A DNTTIP2 DPH2 DRAP1 DSG2
10-DEBC     0       0    0    0    0     0     0    -4   0     0      0      0      0      0       3   -3     0     0      0       0    0    -3    0
        DUSP11 DUSP14 DUSP22 DUSP3 DUSP4 DUSP6 DYNLT3 DYRK3 E2F2 EAPP EBNA1BP2 EBP ECD ECH1 EDEM1 EDN1 EED EGF EGFR EGR1 EIF4EBP1 EIF4G1 EIF5 ELAC2
10-DEBC      3      0      0     0     0     0      0     0    0    0        0   0  -3    0     0    0   0   0    0    0        0      0    0    -3
        ELAVL1 ELOVL6 EML3 ENOPH1 ENOSF1 EPB41L2 EPHA3 EPHB2 EPN2 EPRS ERBB2 ERBB3 ETFB ETS1 ETV1 EVL EXOSC4 EXT1 EZH2 FAH FAIM FAM20B FAM57A FAM63A
10-DEBC      0      0   -3      0      0      -3     0     0    0    0     0     0    0    0    0   0      0    0   -3   0    3      0      0      0
        FAM69A FAS FASTKD5 FAT1 FBXL12 FBXO11 FBXO21 FBXO7 FCHO1 FDFT1 FEZ2 FGFR2 FGFR4 FHL2 FIS1 FKBP14 FKBP4 FOS FOSL1 FOXJ3 FOXO3 FOXO4 FPGS FRS2
10-DEBC      0   0       0    0      0      0      0     0     0     0    0     0     0    0    0      0     0   0     0    -3     0     0    0    0
        FSD1 FUT1 FYN FZD1 FZD7 G3BP1 GAA GABPB1 GADD45A GADD45B GALE GAPDH GATA2 GATA3 GDPD5 GFOD1 GFPT1 GHR GLI2 GLOD4 GLRX GMNN GNA11 GNA15 GNAI1
10-DEBC    0    0   0    0    0     0   0      0       0       0    0     0     0     0     0     0    -4   0    0     0    0    0     0     0     0
        GNAI2 GNAS GNB5 GNPDA1 GOLT1B GPATCH8 GPC1 GRB10 GRB7 GRN GRWD1 GSTM2 GSTZ1 GTF2A2 GTF2E2 GTPBP8 H2AFV HADH HAT1 HDAC2 HDAC6 HDGFRP3 HEATR1
10-DEBC     0   -3    0      0      0       0    0     0    0   0     0     0     0      0      0      0     0    0    0     0     0       0      0
        HEBP1 HERC6 HERPUD1 HES1 HIF1A HIST1H2BK HIST2H2BE HK1 HMG20B HMGA2 HMGCR HMGCS1 HMOX1 HN1L HOMER2 HOOK2 HOXA10 HOXA5 HPRT1 HS2ST1 HSD17B10
10-DEBC     0     0       0    0     0         0         0   0     -3     0     0      0     0    0      0     0      0     0     0      3        0
        HSD17B11 HSPA1A HSPA4 HSPA8 HSPB1 HSPD1 HTATSF1 HTRA1 HYOU1 IARS2 ICAM1 ICAM3 ICMT ID2 IDE IER3 IFNAR1 IFRD2 IGF1R IGF2BP2 IGF2R IGFBP3
10-DEBC        0      0     0     0     0     0       0     0     0     0     0     4    0   0   0    0      0     0     0       0     0      0
        IGHMBP2 IKBKAP IKBKB IKBKE IKZF1 IL13RA1 IL1B IL4R ILK INPP1 INPP4B INSIG1 INTS3 IPO13 IQGAP1 ISOC1 ITFG1 ITGAE ITGB1BP1 ITGB5 JMJD6 JUN
10-DEBC       0      0     0     0     0       0    0    0   0     0      0      0     0     0      0     0     0     0        0     0     0   0
        KAT6A KAT6B KCNK1 KCTD5 KDELR2 KDM3A KDM5A KDM5B KEAP1 KIAA0100 KIAA0196 KIAA0355 KIAA0753 KIAA0907 KIAA1033 KIF14 KIF20A KIF2C KIF5C KIT
10-DEBC     0     0     0     0      0     0     0     0     0        0        0        0        0       -4        0     0     -3     0     0   3
        KLHDC2 KLHL21 KLHL9 KTN1 LAGE3 LAMA3 LAP3 LBR LGALS8 LGMN LIG1 LIPA LOXL1 LPAR2 LPGAT1 LRP10 LRPAP1 LRRC16A LRRC41 LSM5 LSM6 LSR LYN LYPLA1
10-DEBC      0      0     0    0     0     0    0   0      0    0    0    0     0     0      0    -3      0       0      0    0    3   0   0      3
        LYRM1 MACF1 MALT1 MAMLD1 MAN2B1 MAP2K5 MAP3K4 MAP4K4 MAP7 MAPK13 MAPK1IP1L MAPK9 MAPKAPK2 MAPKAPK3 MAPKAPK5 MAST2 MAT2A MBNL1 MBNL2 MBOAT7
10-DEBC     0     0     0      0      0      0     -4      0    0      0         0     0        0        0        0     0     0     0     0      0
        MBTPS1 MCM3 MCOLN1 ME2 MEF2C MELK MEST METRN MFSD10 MICALL1 MIF MKNK1 MLEC MLLT11 MMP1 MMP2 MNAT1 MOK MPZL1 MRPL12 MRPL19 MRPS16 MRPS2 MSH6
10-DEBC      0    0      0   0     0    0    0     0      0       0   0     0    0      0    0    0     0   0     0      0      0      0     0    0
        MSRA MTA1 MTF2 MTFR1 MTHFD2 MUC1 MVP MYBL2 MYC MYCBP MYCBP2 MYL9 MYLK MYO10 NARFL NCAPD2 NCK1 NCK2 NCOA3 NENF NET1 NFATC3 NFATC4 NFE2L2 NFIL3
10-DEBC    0    0    0     0      0    0   0     0   0     0      0    0    0    -4     0      0    0    0     0    0    0      0      0      0     0
        NFKB2 NFKBIA NFKBIB NFKBIE NGRN NIPSNAP1 NISCH NIT1 NMT1 NNT NOL3 NOLC1 NOS3 NOSIP NOTCH1 NPC1 NPDC1 NPEPL1 NPRL2 NR1H2 NR2F6 NR3C1 NRAS
10-DEBC     0      0     -3      0    0        0     0    0    0   0    0     0    0     0      0    0     0      0     0     0     0     0    0
        NRIP1 NSDHL NT5DC2 NUCB2 NUDCD3 NUDT9 NUP133 NUP62 NUP85 NUP88 NUP93 NUSAP1 NVL ORC1 OXA1L OXCT1 OXSR1 P4HA2 P4HTM PACSIN3 PAF1 PAFAH1B1
10-DEBC     0     0      0     0      0     0      0     0     0     0     0      0   0    0     0     0     0     0     0       0    0        0
        PAFAH1B3 PAICS PAK1 PAK4 PAK6 PAN2 PAPD7 PARP1 PARP2 PAX8 PCBD1 PCCB PCK2 PCM1 PCMT1 PCNA PDGFA PDHX PDIA5 PDLIM1 PDS5A PECR PEX11A PFKL
10-DEBC        0     0    0    0    0    0     0     0     0    0     0    0    0    0     0    0     0   -3     0      0     0    0      0    0
        PGAM1 PGM1 PGRMC1 PHGDH PHKA1 PHKB PHKG2 PIGB PIH1D1 PIK3C2B PIK3C3 PIK3CA PIK3R3 PIK3R4 PIN1 PIP4K2B PKIG PLA2G15 PLA2G4A PLCB3 PLEKHJ1
10-DEBC     0    0      0     0     0    0     0    0      0       0      0      0      0      0    0       0    0       0       0     0       0
        PLEKHM1 PLK1 PLOD3 PLP2 PLS1 PLSCR1 PLSCR3 PMAIP1 PMM2 PNKP PNP POLB POLD4 POLE2 POLG2 POLR1C POLR2I POLR2K POP4 PPARD PPARG PPIC PPIE PPOX
10-DEBC       0    0     0    0    0      0      0      0    0    0   0    0     0     3     0      0      0      3    0     0     0    3    0    0
        PPP1R13B PPP2R3C PPP2R5A PPP2R5E PRAF2 PRCP PRKACA PRKAG2 PRKCD PRKCH PRKCQ PRKX PROS1 PRPF4 PRR15L PRR7 PRSS23 PRUNE PSIP1 PSMB10 PSMB8
10-DEBC        0       0       0       0     0    0      0      0    -4     0     0    0     0     0      0    0      0     0     0      0     0
        PSMD10 PSMD2 PSMD4 PSMD9 PSME1 PSME2 PSMF1 PSMG1 PSRC1 PTGS2 PTK2 PTK2B PTPN1 PTPN12 PTPN6 PTPRC PTPRF PTPRK PUF60 PWP1 PXMP2 PXN PYCR1 PYGL
10-DEBC      0     0     0     0     0     0     0     0     0     0    0     0     0      0     0     0     0     0     0    0     0   0    -3    0
        RAB11FIP2 RAB21 RAB27A RAB31 RAB4A RAC2 RAD51C RAD9A RAE1 RAI14 RALA RALB RALGDS RAP1GAP RASA1 RB1 RBKS RBM15B RBM34 RBM6 REEP5 RELB RFC2
10-DEBC        -3     0      0     0     0    0      0     0    0     0    0    0      0       0     0   0   -3      0     0   -5     0    0    0
        RFC5 RFNG RFX5 RGS2 RHEB RHOA RNF167 RNH1 RNMT RNPS1 RPA1 RPA2 RPA3 RPIA RPL39L RPN1 RPP38 RPS5 RPS6 RPS6KA1 RRAGA RRP12 RRP1B RRP8 RRS1 RSU1
10-DEBC    0    0    0    0    0    0      0    0    0     0    0    0    0    0      0    0     0    0    0       0     0     0     0    0    0    0
        RTN2 RUVBL1 S100A13 S100A4 SACM1L SATB1 SCAND1 SCARB1 SCCPDH SCP2 SCRN1 SCYL3 SDHB SENP6 SERPINE1 SESN1 SFN SGCB SH3BP5 SHB SHC1 SIRT3 SKIV2L
10-DEBC    0      0       0      0      0     0      0      0      0    0     0     0    0     0        0     0   0    0      0   0    0     0     -3
        SKP1 SLC11A2 SLC1A4 SLC25A13 SLC25A14 SLC25A4 SLC25A46 SLC27A3 SLC2A6 SLC35A1 SLC35A3 SLC35B1 SLC35F2 SLC37A4 SLC5A6 SMAD3 SMARCA4 SMARCC1
10-DEBC    0       0      0        0        0       0        0       0      0       0       0       0       0       0      0     0      -3       0
        SMARCD2 SMC1A SMC3 SMC4 SMNDC1 SNAP25 SNCA SNX11 SNX13 SNX6 SNX7 SOCS2 SORBS3 SOX2 SOX4 SPAG4 SPAG7 SPDEF SPEN SPP1 SPR SPRED2 SPTAN1 SPTLC2
10-DEBC       0     0    0    0      0      0    0     0     0    0    0     0      0    0    0     0     0     0   -4    0   0      0      0      0
        SQRDL SQSTM1 SRC SSBP2 ST3GAL5 ST6GALNAC2 ST7 STAMBP STAP2 STAT1 STAT3 STAT5B STK10 STK25 STMN1 STUB1 STX1A STX4 STXBP1 STXBP2 SUPV3L1
10-DEBC     4      0   0     0       0          0   0      0     0     0     0      0     0     0     0     0    -3    0      0      0       0
        SUV39H1 SUZ12 SYK SYNE2 SYNGR3 SYPL1 TARBP1 TATDN2 TBC1D9B TBP TBPL1 TBX2 TBXA2R TCEA2 TCEAL4 TCERG1 TCFL5 TCTA TCTN1 TERF2IP TERT TES TESK1
10-DEBC       0     0   0     0      0     0      0     -3       0   0     0    0      0     0      0     -4     0    0     0       0    0   0     0
        TEX10 TFAP2A TFDP1 TGFB3 TGFBR2 THAP11 TIAM1 TICAM1 TIMELESS TIMM17B TIMM22 TIMM9 TIMP2 TIPARP TJP1 TLE1 TLK2 TLR4 TM9SF2 TM9SF3 TMCO1 TMED10
10-DEBC     0      0     0     0      0      0     0      0        0       0      0     0     0      0    0    0    0    0      0      0     0      0
        TMEM109 TMEM110 TMEM2 TMEM5 TMEM50A TMEM97 TNFRSF21 TNIP1 TOMM34 TOMM70A TOP2A TOPBP1 TOR1A TP53 TP53BP1 TP53BP2 TPD52L2 TPM1 TRAK2 TRAM2
10-DEBC       0       0     0     0       0      0        0     0      0       0     0      0     0    0       0       0       0    0     0     0
        TRAP1 TRAPPC3 TRAPPC6A TRIB1 TRIB3 TRIM13 TRIM2 TSC22D3 TSEN2 TSKU TSPAN3 TSPAN4 TSPAN6 TSTA3 TUBB6 TWF2 TXLNA TXNDC9 TXNL4B TXNRD1 UBE2A
10-DEBC     0       0        0     0     0      0     0       0     0    0      0      0      3     0     0    0     0      0      0     -4     0
        UBE2C UBE2J1 UBE2L6 UBE3B UBE3C UBQLN2 UBR7 UFM1 UGDH USP1 USP14 USP22 USP6NL USP7 UTP14A VAPB VAT1 VAV3 VDAC1 VGLL4 VPS28 VPS72 WASF3 WDR61
10-DEBC     0      0      0     0     0      3    0    0    0    0     0     0      0    0      0    0    0    0     0     0     0     3     0     0
        WDR7 WDTC1 WFS1 WIPF2 WRB XBP1 XPNPEP1 XPO7 YKT6 YME1L1 YTHDF1 ZDHHC6 ZFP36 ZMIZ1 ZMYM2 ZNF131 ZNF274 ZNF318 ZNF395 ZNF451 ZNF586 ZNF589 ZW10
10-DEBC    0     0    0     0   0    0       0    0    0      0      0      0     0     0     0      0      0      0      0      0      0      0    0
 [ reached 'max' / getOption("max.print") -- omitted 5 rows ]
target_compound <- "triptolide"
compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, rownames(compound_sig) %in% rownames(th))
data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data
     ACD    ALDOC   AMDHD2    BUB1B       C5     CBR3     CCL2     CDH3     CHN1   CORO1A     CRYZ     DNM1     EDN1     EGFR     FSD1     FZD1 
       5        5        4        7        7       -3        3        5        4        4       -4        4        7       -6        7        7 
    FZD7     GNB5      HK1    ICAM3    ISOC1    KCNK1    KIF14    LOXL1      LYN   LYPLA1     MSRA    MYBL2      MYC     NOS3     PCK2   PDLIM1 
      -6        7       -5       -5        5       -4       -6        3        6       -5        5        7       -5        5        6        4 
    PLP2     PRKX   PSMB10    PSMB8    PSMG1    PTGS2    PTK2B    PTPRF    PTPRK SERPINE1  SLC27A3   SLC2A6   SLC5A6     SNCA    SOCS2      SYK 
       7        7        4       -3       -7        5        7        7        6        6        6       -3        3        5        7        5 
   TCEA2   TICAM1     TLE1  TOMM70A    TRAK2   UBE2L6    VGLL4 
       7        3       -6       -7       -7        6       -5 
barplot(data, horiz = TRUE, col = "red")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
pdf(file = "triptolide_subset_sig_heatmap.pdf")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()
pdf 
  3 

Now, can we just make a barplot of the spearman correlations?

data <- as.numeric(c(SC.G3, SC.G4, SC.WNT, SC.SHH))
names(data) <- c("G3", "G4", "WNT", "SHH")
data
         G3          G4         WNT         SHH 
-0.16904001  0.05244407  0.02907768  0.05397576 
barplot(data, horiz = TRUE, col = "red")
pdf(file = "triptolide_spearmancorrelation_barplot.pdf")
barplot(data, horiz = TRUE, col = "red")
dev.off()
png 
  2 

Now, it would be pretty cool to cluster the data on this signature and see how it looks…

head(dat)
          G4     G4.1     G4.2     G4.3     G4.4     G4.5     G4.6     G4.7     G4.8     G4.9    G4.10    G4.11    G4.12    G4.13    G4.14    G4.15
1   7.595940 7.806655 7.401414 7.603100 7.996856 7.825205 7.683266 7.457205 7.562213 7.349231 7.692980 6.847049 6.988782 7.347686 7.491087 7.481837
2   6.144400 6.191544 5.907811 6.052795 6.883360 6.283014 5.882486 6.577583 5.841223 6.801283 6.385026 6.321308 6.137943 6.116995 6.906354 6.583686
4   5.670915 5.621487 5.978379 5.599533 5.769882 5.278115 5.732694 5.846439 5.827768 5.992464 5.660527 5.930387 5.950121 5.687315 6.205769 5.967428
14  6.035960 5.816218 6.104124 5.679490 6.089272 5.871273 5.993961 6.450154 6.602588 5.420535 6.050676 5.884714 5.613128 6.012981 5.631928 6.933715
156 3.384390 3.044523 3.629660 3.077312 3.653252 3.126760 3.025291 3.091043 3.711130 3.363842 3.660994 3.161247 3.871201 4.003690 3.779634 4.096010
263 4.891101 3.517498 3.303217 3.462606 3.508556 3.624341 4.385770 4.837075 3.325036 3.380995 3.558201 3.468856 4.508659 3.246491 4.514151 4.326778
       G4.16    G4.17    G4.18    G4.19    G4.20    G4.21    G4.22    G4.23    G4.24    G4.25    G4.26    G4.27    G4.28    G4.29    G4.30    G4.31
1   7.670195 7.220520 7.658086 7.767983 6.940416 7.127614 6.386037 7.178317 7.387895 7.024382 7.156177 7.432957 6.742055 7.073693 7.285918 6.946303
2   6.274951 6.270232 6.959778 6.529857 6.283947 6.006599 6.608406 5.874931 6.296741 6.148041 6.606785 5.929855 6.291013 7.048820 6.531606 6.224955
4   5.742362 5.824524 5.388158 6.076265 6.026107 5.838604 5.771130 5.280153 5.179534 5.875493 5.623295 5.231109 5.210578 5.786283 5.412539 5.220356
14  6.013471 5.510198 5.909169 5.633718 5.349486 5.896329 5.532203 5.838314 6.545781 6.066804 5.773309 5.889155 5.719328 5.975335 5.530222 6.104347
156 3.708682 3.157000 3.742420 3.624341 3.914021 3.487375 3.686376 3.841601 3.186353 3.931826 3.797734 3.493473 4.259859 3.104587 3.747148 3.095578
263 3.505557 4.197202 4.027136 4.432006 3.394508 3.122365 3.698830 3.602777 3.627004 4.403054 3.152736 3.173878 3.310543 3.758872 3.292126 3.449988
       G4.32    G4.33    G4.34    G4.35    G4.36    G4.37    G4.38       G3     G3.1     G3.2     G3.3     G3.4     G3.5     G3.6     G3.7     G3.8
1   7.805026 7.751303 7.649788 7.330798 7.500640 7.667673 7.757735 7.792349 8.260027 7.332892 7.128977 6.899421 6.170656 7.302496 7.727711 7.287560
2   6.617671 6.372637 6.606785 5.766757 6.388730 6.606110 6.893149 6.579529 7.080868 6.642747 6.012002 6.596873 6.690097 6.358189 6.204356 6.734591
4   5.660875 5.980151 5.861640 5.938591 5.984188 5.436774 6.090857 6.212406 6.282827 6.110358 5.918625 6.018593 5.894954 5.746522 6.061457 5.905362
14  5.792709 6.765039 6.683861 6.286184 5.593596 5.412092 6.150390 6.256134 6.440149 5.957132 6.131661 5.810243 7.059016 5.754158 6.413131 7.300203
156 3.735286 3.446808 3.157000 3.226844 3.100092 3.034953 3.173878 3.716008 3.770459 3.449988 3.139832 3.624341 3.535145 3.015535 3.605498 3.555348
263 3.718438 3.182212 3.325036 3.258096 3.363842 3.265759 3.538057 3.194583 3.317816 3.397858 3.178054 3.972177 3.190476 3.374169 3.992681 4.104295
        G3.9    G3.10    G3.11    G3.12    G3.13    G3.14    G3.15      WNT    WNT.1    WNT.2    WNT.3    WNT.4    WNT.5    WNT.6    WNT.7      SHH
1   6.780603 7.560757 6.719979 7.536524 6.942350 7.408894 6.756235 7.600802 7.725507 6.760878 7.165107 6.799502 7.647977 6.919091 6.641443 7.545496
2   6.830982 6.795929 7.313420 6.337003 6.025624 6.564560 6.335409 5.974064 6.624198 6.735305 6.163946 6.448573 6.202940 6.602316 6.553648 6.178773
4   5.780435 5.378514 5.666773 5.862210 5.369708 5.897429 5.580861 5.785977 5.922650 5.800607 5.441985 5.772686 5.318610 5.808143 5.411200 6.218002
14  7.105622 5.085124 6.742763 6.637520 5.778890 5.557214 5.903998 6.738745 6.490875 6.491330 6.100095 6.589751 5.998937 6.041920 5.840641 6.991361
156 4.041296 3.284664 3.049273 3.058707 3.117950 4.007333 4.067316 3.117950 3.254243 3.756538 4.019980 3.832980 3.879500 3.314186 3.310543 3.901973
263 3.906005 3.484312 3.222868 3.238678 3.856510 3.770459 3.511545 3.380995 3.250375 3.242592 3.280911 3.131137 3.325036 3.126760 3.332205 3.610918
       SHH.1    SHH.2    SHH.3    SHH.4    SHH.5    SHH.6    SHH.7    SHH.8    SHH.9 Gene.Symbol
1   7.937874 7.673595 6.877605 6.945340 7.776745 7.462502 7.460433 7.466914 7.750744        DDR1
2   6.507725 6.100991 6.377067 6.315358 6.776963 6.173369 6.482343 6.058188 6.541607        RFC2
4   5.592478 5.796361 6.023205 5.615680 5.797880 5.792709 5.859931 5.993961 6.115450        PAX8
14  6.294343 6.667593 7.128335 6.386711 6.940416 6.477126 5.790877 6.324000 6.066108      SCARB1
156 3.629660 3.072693 3.303217 3.895894 3.374169 3.921973 3.929863 3.740048 3.788725       PTPRC
263 3.292126 3.182212 3.629660 3.475067 3.269569 3.242592 4.266896 3.242592 3.437208       JMJD6
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct
head(dat2)
rownames(dat2) <- dat2$Gene.Symbol
Setting row names on a tibble is deprecated.
# MedulloSigs <- dat2
# rm(dat)
# rm(dat2)
head(dat2)
names(cmpd_ordered)
  [1] "ABCF1"      "ABCF3"      "ABHD6"      "ABL1"       "ACAA1"      "ACBD3"      "ACD"        "ACLY"       "ACOT9"      "ADAM10"     "ADAT1"     
 [12] "ADCK3"      "ADH5"       "ADI1"       "ADO"        "AGL"        "AKAP8"      "AKAP8L"     "ALAS1"      "ALDH7A1"    "ALDOC"      "AMDHD2"    
 [23] "ANO10"      "ANXA7"      "APBB2"      "APOE"       "APPBP2"     "ARFIP2"     "ARHGAP1"    "ARHGEF12"   "ARHGEF2"    "ARID4B"     "ARID5B"    
 [34] "ARL4C"      "ARNT2"      "ARPP19"     "ASAH1"      "ASCC3"      "ATF1"       "ATF5"       "ATG3"       "ATMIN"      "ATP11B"     "ATP1B1"    
 [45] "ATP2C1"     "ATP5S"      "ATP6V0B"    "AURKA"      "AURKB"      "BACE2"      "BAD"        "BAG3"       "BAMBI"      "BAX"        "BCL2"      
 [56] "BCL7B"      "BHLHE40"    "BID"        "BIRC2"      "BLCAP"      "BLMH"       "BLVRA"      "BMP4"       "BNIP3"      "BNIP3L"     "BPHL"      
 [67] "BRCA1"      "BTK"        "BUB1B"      "C2CD2"      "C2CD2L"     "C5"         "CAB39"      "CALM3"      "CALU"       "CAMSAP2"    "CANT1"     
 [78] "CASC3"      "CASK"       "CASP10"     "CASP2"      "CASP3"      "CASP7"      "CAST"       "CAT"        "CBLB"       "CBR1"       "CBR3"      
 [89] "CCDC92"     "CCL2"       "CCNA1"      "CCNA2"      "CCNB1"      "CCNB2"      "CCND3"      "CCNF"       "CCNH"       "CCP110"     "CD320"     
[100] "CD40"       "CD44"       "CDC20"      "CDC25A"     "CDC25B"     "CDC42"      "CDC45"      "CDCA4"      "CDH3"       "CDK1"       "CDK19"     
[111] "CDK4"       "CDK5R1"     "CDK7"       "CDKN1B"     "CDKN2A"     "CEBPD"      "CEBPZ"      "CENPE"      "CERK"       "CGRRF1"     "CHAC1"     
[122] "CHEK1"      "CHEK2"      "CHERP"      "CHIC2"      "CHMP6"      "CHN1"       "CLIC4"      "CLPX"       "CLTB"       "CLTC"       "CNDP2"     
[133] "CNOT4"      "CNPY3"      "COG4"       "COG7"       "COL1A1"     "COPB2"      "COPS7A"     "CORO1A"     "CPNE3"      "CPSF4"      "CREG1"     
[144] "CRELD2"     "CRK"        "CRKL"       "CRTAP"      "CRYZ"       "CSK"        "CSNK1A1"    "CSNK1E"     "CSNK2A2"    "CSRP1"      "CTNND1"    
[155] "CTSD"       "CXCR4"      "CYCS"       "CYTH1"      "DAXX"       "DCK"        "DCUN1D4"    "DDB2"       "DDR1"       "DDX10"      "DDX42"     
[166] "DECR1"      "DFFA"       "DFFB"       "DHDDS"      "DHRS7"      "DHX29"      "DLD"        "DMTF1"      "DNAJA3"     "DNAJB1"     "DNAJB6"    
[177] "DNM1"       "DNMT1"      "DNTTIP2"    "DPH2"       "DUSP11"     "DUSP14"     "DYRK3"      "E2F2"       "EAPP"       "EBNA1BP2"   "EBP"       
[188] "ECD"        "ECH1"       "EDEM1"      "EDN1"       "EED"        "EGF"        "EGFR"       "EIF4G1"     "EIF5"       "ELAC2"      "ELOVL6"    
[199] "EML3"       "ENOPH1"     "EPHA3"      "EPHB2"      "EPN2"       "EPRS"       "ERBB2"      "ETS1"       "EVL"        "EXT1"       "EZH2"      
[210] "FAH"        "FAIM"       "FAM20B"     "FAM57A"     "FAM63A"     "FAM69A"     "FAS"        "FASTKD5"    "FBXL12"     "FBXO11"     "FBXO21"    
[221] "FBXO7"      "FCHO1"      "FDFT1"      "FEZ2"       "FGFR2"      "FGFR4"      "FHL2"       "FKBP14"     "FKBP4"      "FOS"        "FOSL1"     
[232] "FOXJ3"      "FOXO3"      "FOXO4"      "FRS2"       "FSD1"       "FUT1"       "FZD1"       "FZD7"       "G3BP1"      "GAA"        "GABPB1"    
[243] "GADD45A"    "GADD45B"    "GALE"       "GAPDH"      "GDPD5"      "GFOD1"      "GLI2"       "GLOD4"      "GLRX"       "GMNN"       "GNA11"     
[254] "GNA15"      "GNAS"       "GNB5"       "GOLT1B"     "GPATCH8"    "GPC1"       "GRB7"       "GRN"        "GRWD1"      "GSTM2"      "GSTZ1"     
[265] "GTF2A2"     "GTF2E2"     "GTPBP8"     "H2AFV"      "HAT1"       "HDAC2"      "HEATR1"     "HERC6"      "HIF1A"      "HIST1H2BK"  "HIST2H2BE" 
[276] "HK1"        "HMGCR"      "HMGCS1"     "HMOX1"      "HN1L"       "HOMER2"     "HOOK2"      "HOXA10"     "HOXA5"      "HS2ST1"     "HSPA1A"    
[287] "HSPA4"      "HSPA8"      "HSPD1"      "HTATSF1"    "HTRA1"      "HYOU1"      "IARS2"      "ICAM1"      "ICAM3"      "ID2"        "IDE"       
[298] "IER3"       "IFNAR1"     "IFRD2"      "IGF1R"      "IGF2BP2"    "IGF2R"      "IGFBP3"     "IGHMBP2"    "IKBKAP"     "IKBKB"      "IKBKE"     
[309] "IKZF1"      "IL13RA1"    "IL1B"       "IL4R"       "INPP1"      "INPP4B"     "INSIG1"     "INTS3"      "IPO13"      "IQGAP1"     "ISOC1"     
[320] "ITFG1"      "ITGAE"      "ITGB5"      "JMJD6"      "JUN"        "KAT6A"      "KCNK1"      "KCTD5"      "KDM3A"      "KDM5A"      "KDM5B"     
[331] "KIAA0196"   "KIAA0355"   "KIAA0753"   "KIAA0907"   "KIAA1033"   "KIF14"      "KIF20A"     "KIF2C"      "KIF5C"      "KIT"        "LAGE3"     
[342] "LAP3"       "LBR"        "LGALS8"     "LGMN"       "LOXL1"      "LPAR2"      "LPGAT1"     "LRPAP1"     "LSM5"       "LSM6"       "LSR"       
[353] "LYN"        "LYPLA1"     "MACF1"      "MAN2B1"     "MAP2K5"     "MAP3K4"     "MAP4K4"     "MAPK1IP1L"  "MAPK9"      "MAPKAPK2"   "MAPKAPK3"  
[364] "MAPKAPK5"   "MAT2A"      "MBNL1"      "MBNL2"      "MBTPS1"     "MCM3"       "MCOLN1"     "MELK"       "MEST"       "MICALL1"    "MKNK1"     
[375] "MMP1"       "MMP2"       "MNAT1"      "MPZL1"      "MRPL12"     "MRPL19"     "MRPS16"     "MRPS2"      "MSH6"       "MSRA"       "MTA1"      
[386] "MTF2"       "MTFR1"      "MTHFD2"     "MVP"        "MYBL2"      "MYC"        "MYCBP2"     "MYL9"       "MYO10"      "NARFL"      "NCAPD2"    
[397] "NCK1"       "NCK2"       "NCOA3"      "NENF"       "NET1"       "NFATC4"     "NFE2L2"     "NFKB2"      "NFKBIA"     "NFKBIB"     "NFKBIE"    
[408] "NGRN"       "NISCH"      "NIT1"       "NOL3"       "NOLC1"      "NOS3"       "NOTCH1"     "NPC1"       "NPDC1"      "NPEPL1"     "NPRL2"     
[419] "NR1H2"      "NR2F6"      "NRIP1"      "NSDHL"      "NT5DC2"     "NUCB2"      "NUDCD3"     "NUDT9"      "NUP62"      "NUP85"      "NUP88"     
[430] "NUSAP1"     "NVL"        "ORC1"       "OXA1L"      "OXCT1"      "OXSR1"      "P4HTM"      "PAF1"       "PAFAH1B1"   "PAICS"      "PAPD7"     
[441] "PARP2"      "PAX8"       "PCCB"       "PCK2"       "PCM1"       "PCMT1"      "PCNA"       "PDGFA"      "PDHX"       "PDLIM1"     "PDS5A"     
[452] "PECR"       "PFKL"       "PGM1"       "PHKA1"      "PHKB"       "PHKG2"      "PIH1D1"     "PIK3C2B"    "PIK3CA"     "PIK3R3"     "PIK3R4"    
[463] "PIP4K2B"    "PLA2G4A"    "PLCB3"      "PLEKHM1"    "PLK1"       "PLOD3"      "PLP2"       "PLS1"       "PMAIP1"     "PMM2"       "PNP"       
[474] "POLD4"      "POLE2"      "POLG2"      "POLR1C"     "POLR2K"     "POP4"       "PPARD"      "PPOX"       "PPP1R13B"   "PPP2R3C"    "PPP2R5E"   
[485] "PRCP"       "PRKACA"     "PRKCQ"      "PRKX"       "PROS1"      "PRPF4"      "PRR15L"     "PRR7"       "PRSS23"     "PRUNE"      "PSIP1"     
[496] "PSMB10"     "PSMB8"      "PSMD10"     "PSMD2"      "PSMD4"      "PSMD9"      "PSMF1"      "PSMG1"      "PSRC1"      "PTGS2"      "PTK2"      
[507] "PTK2B"      "PTPN1"      "PTPN12"     "PTPRC"      "PTPRF"      "PTPRK"      "PUF60"      "PWP1"       "PXN"        "RAB21"      "RAB27A"    
[518] "RAB31"      "RAB4A"      "RAC2"       "RAD51C"     "RAD9A"      "RAE1"       "RAI14"      "RALA"       "RALB"       "RAP1GAP"    "RASA1"     
[529] "RBKS"       "RBM15B"     "RBM34"      "RBM6"       "RFNG"       "RFX5"       "RGS2"       "RHEB"       "RNH1"       "RNMT"       "RNPS1"     
[540] "RPA2"       "RPA3"       "RPL39L"     "RPP38"      "RPS5"       "RPS6"       "RRAGA"      "RRP12"      "RRP1B"      "RRP8"       "RSU1"      
[551] "RTN2"       "RUVBL1"     "SACM1L"     "SCAND1"     "SCARB1"     "SCCPDH"     "SCP2"       "SCYL3"      "SDHB"       "SENP6"      "SERPINE1"  
[562] "SFN"        "SGCB"       "SHB"        "SHC1"       "SIRT3"      "SLC11A2"    "SLC25A13"   "SLC25A46"   "SLC27A3"    "SLC2A6"     "SLC35A3"   
[573] "SLC35B1"    "SLC35F2"    "SLC37A4"    "SLC5A6"     "SMAD3"      "SMARCA4"    "SMARCC1"    "SMC3"       "SMC4"       "SMNDC1"     "SNAP25"    
[584] "SNCA"       "SNX11"      "SNX13"      "SNX7"       "SOCS2"      "SOX2"       "SOX4"       "SPAG4"      "SPAG7"      "SPDEF"      "SPEN"      
[595] "SPR"        "SPRED2"     "SPTAN1"     "SPTLC2"     "SQRDL"      "SQSTM1"     "SRC"        "SSBP2"      "ST3GAL5"    "ST6GALNAC2" "ST7"       
[606] "STAMBP"     "STAP2"      "STAT5B"     "STK10"      "STUB1"      "STX4"       "STXBP1"     "STXBP2"     "SUPV3L1"    "SUV39H1"    "SUZ12"     
[617] "SYK"        "SYNE2"      "SYPL1"      "TARBP1"     "TATDN2"     "TBP"        "TBPL1"      "TBX2"       "TBXA2R"     "TCEA2"      "TCERG1"    
[628] "TCTA"       "TCTN1"      "TERF2IP"    "TERT"       "TES"        "TESK1"      "TFAP2A"     "TGFB3"      "TGFBR2"     "THAP11"     "TICAM1"    
[639] "TIMELESS"   "TIMM17B"    "TIMM22"     "TIMM9"      "TIMP2"      "TIPARP"     "TJP1"       "TLE1"       "TLR4"       "TM9SF2"     "TMED10"    
[650] "TMEM110"    "TMEM2"      "TMEM5"      "TMEM50A"    "TMEM97"     "TOMM70A"    "TOP2A"      "TOR1A"      "TP53BP1"    "TP53BP2"    "TPD52L2"   
[661] "TPM1"       "TRAK2"      "TRAM2"      "TRAP1"      "TRAPPC3"    "TRAPPC6A"   "TRIB3"      "TRIM13"     "TRIM2"      "TSEN2"      "TSKU"      
[672] "TUBB6"      "TWF2"       "TXLNA"      "TXNDC9"     "TXNRD1"     "UBE2C"      "UBE2J1"     "UBE2L6"     "UBE3B"      "UBR7"       "USP1"      
[683] "USP14"      "USP22"      "USP6NL"     "USP7"       "VAT1"       "VAV3"       "VDAC1"      "VGLL4"      "VPS28"      "VPS72"      "WASF3"     
[694] "WDR61"      "WDR7"       "WIPF2"      "WRB"        "XBP1"       "XPNPEP1"    "XPO7"       "YKT6"       "YTHDF1"     "ZDHHC6"     "ZFP36"     
[705] "ZMYM2"      "ZNF131"     "ZNF395"     "ZNF589"     "ZW10"      
dat3 <- subset(dat2, rownames(dat2) %in% rownames(compound_sig))
dat4<-dat3
dat4$Gene.Symbol <- NULL
rownames(dat4) <- dat3$Gene.Symbol
Setting row names on a tibble is deprecated.
# rownames(dat3) <- dat3$Gene.Symbol
# dat3$Gene.Symbol <- NULL
pheatmap::pheatmap(dat4, scale = "row")

# How can we annotate this real quick. 
g <- as.data.frame(colnames(dat4))
g
   colnames(dat4)
1              G4
2            G4.1
3            G4.2
4            G4.3
5            G4.4
6            G4.5
7            G4.6
8            G4.7
9            G4.8
10           G4.9
11          G4.10
12          G4.11
13          G4.12
14          G4.13
15          G4.14
16          G4.15
17          G4.16
18          G4.17
19          G4.18
20          G4.19
21          G4.20
22          G4.21
23          G4.22
24          G4.23
25          G4.24
26          G4.25
27          G4.26
28          G4.27
29          G4.28
30          G4.29
31          G4.30
32          G4.31
33          G4.32
34          G4.33
35          G4.34
36          G4.35
37          G4.36
38          G4.37
39          G4.38
40             G3
41           G3.1
42           G3.2
43           G3.3
44           G3.4
45           G3.5
46           G3.6
47           G3.7
48           G3.8
49           G3.9
50          G3.10
51          G3.11
52          G3.12
53          G3.13
54          G3.14
55          G3.15
56            WNT
57          WNT.1
58          WNT.2
59          WNT.3
60          WNT.4
61          WNT.5
62          WNT.6
63          WNT.7
64            SHH
65          SHH.1
66          SHH.2
67          SHH.3
68          SHH.4
69          SHH.5
70          SHH.6
71          SHH.7
72          SHH.8
73          SHH.9
for (i in 1:length(g$`colnames(dat4)`)){
  g$type[i] <- unlist(strsplit(as.character(g$`colnames(dat4)`[i]), split = ".", fixed = TRUE))[[1]]
}
g
   colnames(dat4) type
1              G4   G4
2            G4.1   G4
3            G4.2   G4
4            G4.3   G4
5            G4.4   G4
6            G4.5   G4
7            G4.6   G4
8            G4.7   G4
9            G4.8   G4
10           G4.9   G4
11          G4.10   G4
12          G4.11   G4
13          G4.12   G4
14          G4.13   G4
15          G4.14   G4
16          G4.15   G4
17          G4.16   G4
18          G4.17   G4
19          G4.18   G4
20          G4.19   G4
21          G4.20   G4
22          G4.21   G4
23          G4.22   G4
24          G4.23   G4
25          G4.24   G4
26          G4.25   G4
27          G4.26   G4
28          G4.27   G4
29          G4.28   G4
30          G4.29   G4
31          G4.30   G4
32          G4.31   G4
33          G4.32   G4
34          G4.33   G4
35          G4.34   G4
36          G4.35   G4
37          G4.36   G4
38          G4.37   G4
39          G4.38   G4
40             G3   G3
41           G3.1   G3
42           G3.2   G3
43           G3.3   G3
44           G3.4   G3
45           G3.5   G3
46           G3.6   G3
47           G3.7   G3
48           G3.8   G3
49           G3.9   G3
50          G3.10   G3
51          G3.11   G3
52          G3.12   G3
53          G3.13   G3
54          G3.14   G3
55          G3.15   G3
56            WNT  WNT
57          WNT.1  WNT
58          WNT.2  WNT
59          WNT.3  WNT
60          WNT.4  WNT
61          WNT.5  WNT
62          WNT.6  WNT
63          WNT.7  WNT
64            SHH  SHH
65          SHH.1  SHH
66          SHH.2  SHH
67          SHH.3  SHH
68          SHH.4  SHH
69          SHH.5  SHH
70          SHH.6  SHH
71          SHH.7  SHH
72          SHH.8  SHH
73          SHH.9  SHH
e <- g
rownames(e) <- g$`colnames(dat4)`
e
      colnames(dat4) type
G4                G4   G4
G4.1            G4.1   G4
G4.2            G4.2   G4
G4.3            G4.3   G4
G4.4            G4.4   G4
G4.5            G4.5   G4
G4.6            G4.6   G4
G4.7            G4.7   G4
G4.8            G4.8   G4
G4.9            G4.9   G4
G4.10          G4.10   G4
G4.11          G4.11   G4
G4.12          G4.12   G4
G4.13          G4.13   G4
G4.14          G4.14   G4
G4.15          G4.15   G4
G4.16          G4.16   G4
G4.17          G4.17   G4
G4.18          G4.18   G4
G4.19          G4.19   G4
G4.20          G4.20   G4
G4.21          G4.21   G4
G4.22          G4.22   G4
G4.23          G4.23   G4
G4.24          G4.24   G4
G4.25          G4.25   G4
G4.26          G4.26   G4
G4.27          G4.27   G4
G4.28          G4.28   G4
G4.29          G4.29   G4
G4.30          G4.30   G4
G4.31          G4.31   G4
G4.32          G4.32   G4
G4.33          G4.33   G4
G4.34          G4.34   G4
G4.35          G4.35   G4
G4.36          G4.36   G4
G4.37          G4.37   G4
G4.38          G4.38   G4
G3                G3   G3
G3.1            G3.1   G3
G3.2            G3.2   G3
G3.3            G3.3   G3
G3.4            G3.4   G3
G3.5            G3.5   G3
G3.6            G3.6   G3
G3.7            G3.7   G3
G3.8            G3.8   G3
G3.9            G3.9   G3
G3.10          G3.10   G3
G3.11          G3.11   G3
G3.12          G3.12   G3
G3.13          G3.13   G3
G3.14          G3.14   G3
G3.15          G3.15   G3
WNT              WNT  WNT
WNT.1          WNT.1  WNT
WNT.2          WNT.2  WNT
WNT.3          WNT.3  WNT
WNT.4          WNT.4  WNT
WNT.5          WNT.5  WNT
WNT.6          WNT.6  WNT
WNT.7          WNT.7  WNT
SHH              SHH  SHH
SHH.1          SHH.1  SHH
SHH.2          SHH.2  SHH
SHH.3          SHH.3  SHH
SHH.4          SHH.4  SHH
SHH.5          SHH.5  SHH
SHH.6          SHH.6  SHH
SHH.7          SHH.7  SHH
SHH.8          SHH.8  SHH
SHH.9          SHH.9  SHH
e$`colnames(dat4)` <- NULL
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)
pdf(file = "triptolide_mb_clusteringHeatmap.pdf")

pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)
dev.off()
pdf 
  3 

---
title: "Obtain and Plot L1000 Signatures"
output: html_notebook
---

```{r}
L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)

head(L1000_signature_data)

target_compound <- "triptolide"

compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, compound_sig$triptolide != 0)

data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data

barplot(data, horiz = TRUE, col = "red")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)

pdf(file = "triptolide_sig_heatmap.pdf")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()
```

# So now subset this signature for genes within different medulloblastoma disease signatures. A good way to pick which one is ideal is to find which one this drug reverses the disease signature most of. 

So let's load in the medulloblastoma disease signature data from Anna. 
- This is a microarray dataset, so some genes have multiple probes. These probes are labeled for specificity, but for this purpose we will just average duplicate rows, so each gene's reported fold-change is representative of all probes for each gene. 

First, we should subset columns that are averagable.. ie. numeric
So Fold-change.

Then we will avverage the fold changes within each gene, and use that to calculate signature overlap with compound response signatures. 

```{r}
library(dplyr)
MedulloSigs <- read.csv(file = "MedulloSigs.csv", skip = 1, header = TRUE)
head(MedulloSigs)

myvars <- c("Gene.Symbol", "Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat <- MedulloSigs[myvars]

myvars2 <- c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct

head(dat2)
rownames(dat2) <- dat2$Gene.Symbol

MedulloSigs <- dat2
rm(dat)
rm(dat2)
```

# Now, let's subset this medullo data for the genes that are in the compound response signature. Then, we can assess differential discordance. 

```{r}
head(MedulloSigs)
```

```{r}
head(compound_sig)
cmpdGenes <- rownames(compound_sig)
  # obj.transpose <- t(obj@assays$SCT@scale.data) 
  cmpd_overlap <- rownames(MedulloSigs)[which(rownames(MedulloSigs) %in% cmpdGenes)]
  overlap <- MedulloSigs[cmpd_overlap,] # FileA
  overlap
  rownames(overlap) <- overlap$Gene.Symbol
  
  # overlap$Gene.Symbol <- NULL
  head(overlap)
  
  cmpd_ordered <- as.numeric(as.vector(t(compound_sig)))
  names(cmpd_ordered) <- rownames(compound_sig)
  cmpd_ordered
  cmpd_ordered2 <- cmpd_ordered[cmpd_overlap] # Character list in brackets orders to fit that character list...
  
  cmpd_ordered2
  
  print("Check that genes are all in the right order... ")
  head(rownames(overlap) == names(cmpd_ordered2))
  
  #
  head(rownames(overlap))
  head(names(cmpd_ordered2))
  
```

# Now set up each different tumor type as a vector or whatever to be able to calculate SC for each...  
  
```{r}

# SHH
head(overlap)
SHH <- overlap$Log2FC_SHH
names(SHH) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(SHH) == names(cmpd_ordered2))

SC.SHH <- cor(cmpd_ordered2, SHH, method = "spearman")
  
# WNT
head(overlap)
WNT <- overlap$Log2FC_WNT
names(WNT) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(WNT) == names(cmpd_ordered2))

SC.WNT <- cor(cmpd_ordered2, WNT, method = "spearman")

# G3
head(overlap)
G3 <- overlap$Log2FC_G3
names(G3) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(G3) == names(cmpd_ordered2))

SC.G3 <- cor(cmpd_ordered2, G3, method = "spearman")

# G4
head(overlap)
G4 <- overlap$Log2FC_G4
names(G4) <- rownames(overlap)  
  
# Check that everything is still in the right order here...
print("Check that genes are all in the right order... ")
head(names(G4) == names(cmpd_ordered2))

SC.G4 <- cor(cmpd_ordered2, G4, method = "spearman")

```

# So how do we make a figure showing that g3 is predicted over SHH, others?

First, can we subset to a signature that we can visualize by thresholding on fold change?

```{r}
G3

df <- as.data.frame(G3)
df

th <- subset(df, df$G3 > 0.1 | df$G3 < -0.1)

th

L1000_signature_data <- read.table(file = "matPH3_2_1_0.2_0.3_L1000_Batch2017_Regina_removed.txt", row.names = 1, header = TRUE)

head(L1000_signature_data)

target_compound <- "triptolide"

compound_sig <- as.data.frame(t(subset(L1000_signature_data, rownames(L1000_signature_data) == target_compound)))
compound_sig <- subset(compound_sig, rownames(compound_sig) %in% rownames(th))

data <- compound_sig$triptolide
names(data) <- rownames(compound_sig)
data

barplot(data, horiz = TRUE, col = "red")

pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)

pdf(file = "triptolide_subset_sig_heatmap.pdf")
pheatmap::pheatmap(compound_sig, cluster_cols = FALSE)
dev.off()
```

# Now, can we just make a barplot of the spearman correlations?

```{r}
data <- as.numeric(c(SC.G3, SC.G4, SC.WNT, SC.SHH))
names(data) <- c("G3", "G4", "WNT", "SHH")
data

barplot(data, horiz = TRUE, col = "red")
pdf(file = "triptolide_spearmancorrelation_barplot.pdf")
barplot(data, horiz = TRUE, col = "red")
dev.off()
```

# Now, it would be pretty cool to cluster the data on this signature and see how it looks...

```{r}
library(dplyr)
MedulloSigs <- read.csv(file = "MedulloSigs.csv", skip = 1, header = TRUE)
head(MedulloSigs)

'%nin%' = Negate('%in%')
cols <- colnames(MedulloSigs)
cols
myvars <- subset(cols, cols %nin% c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH", "MEDIAN_OVERALL", "MEDIAN_G4", "MEDIAN_G3", "MEDIAN_WNT", "MEDIAN_SHH", "X.1", "Probe.Set.ID", "X.2", "X.3", "X.4", "X.5", "X.6", "X.7", "X"))
dat <- MedulloSigs[myvars]
# head(dat)
# myvars2 <- c("Log2FC_G4", "Log2FC_G3", "Log2FC_WNT", "Log2FC_SHH")
# rownames(dat) <- dat$Gene.Symbol
dat <- subset(dat, dat$Gene.Symbol %in% colnames(L1000_signature_data))
head(dat)
```

```{r}
dat2 <- dat %>% group_by(Gene.Symbol) %>% mutate_each(funs(mean), -(0)) %>% distinct

head(dat2)
rownames(dat2) <- dat2$Gene.Symbol

# MedulloSigs <- dat2
# rm(dat)
# rm(dat2)

head(dat2)

names(cmpd_ordered)

dat3 <- subset(dat2, rownames(dat2) %in% rownames(compound_sig))

dat4<-dat3
dat4$Gene.Symbol <- NULL
rownames(dat4) <- dat3$Gene.Symbol

# rownames(dat3) <- dat3$Gene.Symbol
# dat3$Gene.Symbol <- NULL
pheatmap::pheatmap(dat4, scale = "row")

# How can we annotate this real quick. 

g <- as.data.frame(colnames(dat4))
g
for (i in 1:length(g$`colnames(dat4)`)){
  g$type[i] <- unlist(strsplit(as.character(g$`colnames(dat4)`[i]), split = ".", fixed = TRUE))[[1]]
}
g
e <- g
rownames(e) <- g$`colnames(dat4)`
e
e$`colnames(dat4)` <- NULL
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)

pdf(file = "triptolide_mb_clusteringHeatmap.pdf")
pheatmap::pheatmap(dat4, scale = "row", annotation_col = e)
dev.off()
```

